diff --git a/- b/- new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/README.md b/README.md index 21ad99487db53fc625d1a4b4e8e2a42c9070dbaa..f913cb228479afc7d69eb7c661ca02e1b60e3bd3 100644 --- a/README.md +++ b/README.md @@ -92,6 +92,21 @@ features: - gene: TYE7 description: TYE7 deletion strain +- applies_to: + - annotated_feature_reprocess_intergenic + - annotated_feature_reprocess_intergenic_analysis + fields: + - name: ir_name + dtype: string + description: >- + Unique identifier of the intergenic region. See + yeast_genome_resources/intergenic_regions_metadata_5_1.csv for details on + the region (location, etc). Note that these intergenic regions are defined + as the region between the end of one ORF and the start of the next, and + are named according to the locus tags of the flanking ORFs (e.g., + YAL001C-YAL002W). A intergenic region is assigned to a promoter only when + the 5' end is continuous with the region. + - applies_to: - annotated_feature - annotated_feature_meta @@ -99,6 +114,8 @@ features: - genome_map_meta - annotated_feature_reprocess_yiming - annotated_feature_reprocess_mindel + - annotated_feature_reprocess_start_codon_500 + - annotated_feature_reprocess_intergenic fields: - name: batch dtype: string @@ -111,6 +128,8 @@ features: - genome_map_meta - 2026_analysis_set - annotated_feature_reprocess_mindel_analysis + - annotated_feature_reprocess_start_codon_500bp_analysis + - annotated_feature_reprocess_intergenic_analysis fields: - name: regulator_locus_tag dtype: string @@ -128,6 +147,10 @@ features: - annotated_feature_reprocess_yiming - annotated_feature_reprocess_mindel - annotated_feature_reprocess_mindel_analysis + - annotated_feature_reprocess_start_codon_500 + - annotated_feature_reprocess_start_codon_500bp_analysis + - annotated_feature_reprocess_intergenic + - annotated_feature_reprocess_intergenic_analysis fields: - name: target_locus_tag dtype: string @@ -145,6 +168,10 @@ features: - annotated_feature_reprocess_yiming - annotated_feature_reprocess_mindel - annotated_feature_reprocess_mindel_analysis + - annotated_feature_reprocess_start_codon_500 + - annotated_feature_reprocess_start_codon_500bp_analysis + - annotated_feature_reprocess_intergenic + - annotated_feature_reprocess_intergenic_analysis fields: - name: experiment_hops dtype: float64 @@ -181,6 +208,10 @@ features: - annotated_feature_reprocess_yiming - annotated_feature_reprocess_mindel - annotated_feature_reprocess_mindel_analysis + - annotated_feature_reprocess_start_codon_500 + - annotated_feature_reprocess_start_codon_500bp_analysis + - annotated_feature_reprocess_intergenic + - annotated_feature_reprocess_intergenic_analysis fields: - name: total_background_hops dtype: float64 @@ -413,7 +444,7 @@ configs: - config_name: genome_map_meta description: Metadata for genome map datasets including regulator information and experimental details dataset_type: metadata - applies_to: ["genome_map", "annotated_feature_reprocess_yiming", "annotated_feature_reprocess_mindel"] + applies_to: ["genome_map", "annotated_feature_reprocess_yiming", "annotated_feature_reprocess_mindel", "annotated_feature_reprocess_start_codon_500", "annotated_feature_reprocess_intergenic"] data_files: - split: train path: genome_map_meta.parquet @@ -484,6 +515,57 @@ configs: description: >- Genome map identifier linking to the genome_map and genome_map_meta dataset +- config_name: annotated_feature_reprocess_start_codon_500 + description: >- + This is the genome_map data quantified against the promoters defined + as 500bp upstream of the start codon for each gene + (see BrentLab/yeast_genome_resources) using + scripts/quantify_regions_500bp_intergenic.R. + dataset_type: annotated_features + data_files: + - split: train + path: annotated_feature_reprocess_start_codon_500/*/*.parquet + genome_resources: + region_sets: + start_codon_500bp: + path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed + join_column: target_locus_tag + partitioning: + enabled: true + partition_by: ["batch"] + path_template: "annotated_feature_reprocess_start_codon_500/batch={batch}/*.parquet" + dataset_info: + features: + - name: genome_map_id + dtype: int64 + description: >- + Genome map identifier linking to the genome_map and genome_map_meta dataset + +- config_name: annotated_feature_reprocess_intergenic + description: >- + This is the genome_map data quantified against the promoters defined + as the full intergenic region upstream of each gene (see + BrentLab/yeast_genome_resources) using scripts/quantify_regions_500bp_intergenic.R. + dataset_type: annotated_features + data_files: + - split: train + path: annotated_feature_reprocess_intergenic/*/*.parquet + genome_resources: + region_sets: + intergenic: + path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv + join_column: ir_name + partitioning: + enabled: true + partition_by: ["batch"] + path_template: "annotated_feature_reprocess_intergenic/batch={batch}/*.parquet" + dataset_info: + features: + - name: genome_map_id + dtype: int64 + description: >- + Genome map identifier linking to the genome_map and genome_map_meta dataset + - config_name: annotated_feature_reprocess_mindel_analysis description: >- This is the analysis set for the mindel data. It is generated using the same logic as the 2026_analysis_set, but using the results from the reprocessing against the mindel promoters. A passing replicate has >=3000 hops had a dto empirical pvalue < 0.01 against either kemmeren or hackett. Where a given regulator had multiple passing replicates, those replicates were combined (see annotated_feature_combined). This dataset should be used when you want to use data that can be reproduced directly from the genome_map data included in this repo, using the mindel promoter definitions. See scripts/quantify_regions.R as well as BrentLab/yeast_comparative_analysis/scripts for details of how this was conducted. @@ -508,6 +590,54 @@ configs: if they have more than 3k hopes (single or combined), then they are included in the analysis set. role: sample_id + +- config_name: annotated_feature_reprocess_start_codon_500bp_analysis + description: >- + This is the analysis set for promoters created with 500bp regions upstream + of the start codon. It uses the same passing replicates as the 2025_analysis_set. see R/scripts/quantify_regions_500bp_intergenic.R for details of how this was conducted. + dataset_type: annotated_features + metadata_fields: ["combined_id","regulator_locus_tag","regulator_symbol", "total_experiment_hops", "total_background_hops"] + data_files: + - split: train + path: annotated_feature_reprocess_start_codon_500bp_analysis.parquet + genome_resources: + region_sets: + start_codon_500bp: + path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed + join_column: target_locus_tag + dataset_info: + features: + - name: combined_id + dtype: string + description: >- + The genome map identifier of either a single passing, or multiple + passing replicates (hyphen-delimited) that were combined for the + 2026 analysis set. + role: sample_id + +- config_name: annotated_feature_reprocess_intergenic_analysis + description: >- + This is the analysis set for promoters created with the full intergenic + region upstream of a given target. It uses the same passing replicates as the 2025_analysis_set. see R/scripts/quantify_regions_500bp_intergenic.R for details of how this was conducted. + dataset_type: annotated_features + metadata_fields: ["combined_id","regulator_locus_tag","regulator_symbol", "total_experiment_hops", "total_background_hops"] + data_files: + - split: train + path: annotated_feature_reprocess_intergenic_analysis.parquet + genome_resources: + region_sets: + intergenic: + path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv + join_column: ir_name + dataset_info: + features: + - name: combined_id + dtype: string + description: >- + The genome map identifier of either a single passing, or multiple + passing replicates (hyphen-delimited) that were combined for the + 2026 analysis set. + role: sample_id --- # Calling Cards diff --git a/annotated_feature_reprocess_intergenic/batch=CS002/part-0.parquet 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sha256:7334d03f684b60f8b1c803e06899b532c51f2c7b40fdf07310b01bda1b694fdf +size 394315 diff --git a/annotated_feature_reprocess_start_codon_500bp_analysis.parquet b/annotated_feature_reprocess_start_codon_500bp_analysis.parquet new file mode 100644 index 0000000000000000000000000000000000000000..3da8e88b70cf526915c0d3a651af7c86f0252240 --- /dev/null +++ b/annotated_feature_reprocess_start_codon_500bp_analysis.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5d305c6af6047c285e536baa010ad8ad912be5f24ac7ba9eb5b21a087cfc2236 +size 9157294 diff --git a/scripts/quantify_regions.R b/scripts/quantify_regions.R index 48cc74cd62af0aa3f757837fd515ed1d4eb4bd2d..9b985a4686e380c34127e515041f8e60262eb202 100644 --- a/scripts/quantify_regions.R +++ b/scripts/quantify_regions.R @@ -625,14 +625,68 @@ background_gr <- read_tsv("~/code/hf/callingcards/adh1_background_ucsc.qbed") |> dplyr::select(chr, start, end, id, score, strand) |> bed_to_granges() -regions_gr <- arrow::read_parquet("~/code/hf/yeast_genome_resources/mindel_promoters.parquet") |> - bed_to_granges() +# regions_gr <- arrow::read_parquet("~/code/hf/yeast_genome_resources/mindel_promoters.parquet") |> +# bed_to_granges() +# +# regions_gr <- regions_gr[!is.na(regions_gr$target_locus_tag)] +# +# +# # # Run analysis with deduplication (default for calling cards) +# results_replicates = map(genome_map_replicate_meta$id, ~{ +# enrichment_analysis( +# experiment_gr = genome_map_replicate_ds |> +# filter(id == .x) |> +# collect() |> +# dplyr::rename(score = depth) |> +# relocate(chr, start, end, id, score, strand) |> +# mutate(depth = scales::rescale(score, to = c(1,1000))) |> +# bed_to_granges(), +# background_gr = background_gr, +# regions_gr = regions_gr, +# deduplicate_experiment = TRUE, +# pseudocount = 0.1 +# ) +# }) +# names(results_replicates) = genome_map_replicate_meta$id +# +# results_replicates_df = bind_rows(map(results_replicates, as_tibble), .id = "genome_map_id") |> +# mutate(genome_map_id = as.integer(genome_map_id)) |> +# left_join(genome_map_replicate_meta, +# by = c("genome_map_id" = "id")) |> +# select(genome_map_id, batch, +# target_locus_tag, target_symbol, experiment_hops, background_hops, +# total_background_hops, total_experiment_hops, +# callingcards_enrichment, +# poisson_pval, log_poisson_pval, poisson_qval, +# hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> +# mutate(genome_map_id = as.integer(genome_map_id)) + +# arrow::write_dataset( +# results_replicates_df, +# path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_mindel", +# format = "parquet", +# partitioning = c("batch"), +# existing_data_behavior = "overwrite", +# compression = "zstd", +# write_statistics = TRUE, +# use_dictionary = c( +# genome_map_id = TRUE +# ) +# ) + +intergenic_regions_gr <- rtracklayer::import("~/code/hf/yeast_genome_resources/intergenic_regions_5_1.bed") +intergenic_meta = read_csv("~/code/hf/yeast_genome_resources/intergenic_regions_metadata_5_1.csv") |> + filter(chr != "chrM") |> + dplyr::select(ir_name, feature_left, feature_right) |> + pivot_longer(-ir_name, names_to = 'side', values_to = 'target_locus_tag') |> + left_join(dplyr::select(genomic_features, target_locus_tag = locus_tag, target_symbol = symbol)) |> + filter(!is.na(target_symbol)) -regions_gr <- regions_gr[!is.na(regions_gr$target_locus_tag)] +intergenic_regions_gr <- intergenic_regions_gr[intergenic_regions_gr$name %in% unique(intergenic_meta$ir_name)] # # Run analysis with deduplication (default for calling cards) -results_replicates = map(genome_map_replicate_meta$id, ~{ +results_replicates_intergenic = map(genome_map_replicate_meta$id, ~{ enrichment_analysis( experiment_gr = genome_map_replicate_ds |> filter(id == .x) |> @@ -642,19 +696,22 @@ results_replicates = map(genome_map_replicate_meta$id, ~{ mutate(depth = scales::rescale(score, to = c(1,1000))) |> bed_to_granges(), background_gr = background_gr, - regions_gr = regions_gr, + regions_gr = intergenic_regions_gr, deduplicate_experiment = TRUE, pseudocount = 0.1 ) }) -names(results_replicates) = genome_map_replicate_meta$id +names(results_replicates_intergenic) = genome_map_replicate_meta$id -results_replicates_df = bind_rows(map(results_replicates, as_tibble), .id = "genome_map_id") |> +results_replicates_df_intergenic = bind_rows(map(results_replicates_intergenic, as_tibble), .id = "genome_map_id") |> mutate(genome_map_id = as.integer(genome_map_id)) |> + dplyr::rename(ir_name = name) |> + left_join(intergenic_meta, relationship = "many-to-many") |> left_join(genome_map_replicate_meta, by = c("genome_map_id" = "id")) |> select(genome_map_id, batch, - target_locus_tag, target_symbol, experiment_hops, background_hops, + target_locus_tag, target_symbol, ir_name, side, + experiment_hops, background_hops, total_background_hops, total_experiment_hops, callingcards_enrichment, poisson_pval, log_poisson_pval, poisson_qval, @@ -662,8 +719,57 @@ results_replicates_df = bind_rows(map(results_replicates, as_tibble), .id = "gen mutate(genome_map_id = as.integer(genome_map_id)) # arrow::write_dataset( -# results_replicates_df, -# path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_mindel", +# results_replicates_df_intergenic, +# path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_intergenic", +# format = "parquet", +# partitioning = c("batch"), +# existing_data_behavior = "overwrite", +# compression = "zstd", +# write_statistics = TRUE, +# use_dictionary = c( +# genome_map_id = TRUE +# ) +# ) + +start_codon_500bp_pr <- rtracklayer::import("~/code/hf/yeast_genome_resources/start_codon_500bp_upstream_promoters.bed") +start_codon_500bp_pr <- start_codon_500bp_pr[seqnames(start_codon_500bp_pr) != "chrM"] + +# # Run analysis with deduplication (default for calling cards) +results_replicates_start_codon_500 = map(genome_map_replicate_meta$id, ~{ + enrichment_analysis( + experiment_gr = genome_map_replicate_ds |> + filter(id == .x) |> + collect() |> + dplyr::rename(score = depth) |> + relocate(chr, start, end, id, score, strand) |> + mutate(depth = scales::rescale(score, to = c(1,1000))) |> + bed_to_granges(), + background_gr = background_gr, + regions_gr = start_codon_500bp_pr, + deduplicate_experiment = TRUE, + pseudocount = 0.1 + ) +}) +names(results_replicates_start_codon_500) = genome_map_replicate_meta$id + +results_replicates_df_start_codon_500 = bind_rows(map(results_replicates_start_codon_500, as_tibble), .id = "genome_map_id") |> + mutate(genome_map_id = as.integer(genome_map_id)) |> + dplyr::rename(target_locus_tag = name) |> + left_join(dplyr::select(genomic_features, target_locus_tag = locus_tag, target_symbol = symbol)) |> + left_join(genome_map_replicate_meta, + by = c("genome_map_id" = "id")) |> + select(genome_map_id, batch, + target_locus_tag, target_symbol, + experiment_hops, background_hops, + total_background_hops, total_experiment_hops, + callingcards_enrichment, + poisson_pval, log_poisson_pval, poisson_qval, + hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> + mutate(genome_map_id = as.integer(genome_map_id)) + +# arrow::write_dataset( +# results_replicates_df_start_codon_500, +# path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_start_codon_500", # format = "parquet", # partitioning = c("batch"), # existing_data_behavior = "overwrite", diff --git a/scripts/quantify_regions_500bp_intergenic.R b/scripts/quantify_regions_500bp_intergenic.R new file mode 100644 index 0000000000000000000000000000000000000000..46fd3c153a4a2278669ba366e93db81939578d2a --- /dev/null +++ b/scripts/quantify_regions_500bp_intergenic.R @@ -0,0 +1,666 @@ +# Calling Cards Region Quantification +# Quantifies enrichment of insertions/hops in genomic regions +# +# This script: +# 1. Counts insertions overlapping each genomic region (experiment and background) +# 2. Calculates enrichment scores +# 3. Computes Poisson and hypergeometric p-values +# +# Works with any data in BED3+ format (chr, start, end, ...) +# For calling cards: each insertion is counted once regardless of depth +# +# COORDINATE SYSTEMS: +# - Input BED files are assumed to be 0-indexed, half-open [start, end) +# - GenomicRanges uses 1-indexed, closed [start, end] +# - Conversion: GR_start = BED_start + 1, GR_end = BED_end +# +# Usage: +# Rscript quantify_regions.R + +library(tidyverse) +library(GenomicRanges) + +# Statistical Functions --------------------------------------------------- + +#' Calculate enrichment (calling cards effect) +#' +#' @param total_background_hops Total number of hops in background (scalar or vector) +#' @param total_experiment_hops Total number of hops in experiment (scalar or vector) +#' @param background_hops Number of hops in background per region (vector) +#' @param experiment_hops Number of hops in experiment per region (vector) +#' @param pseudocount Pseudocount to avoid division by zero (default: 0.1) +#' @return Enrichment values +calculate_enrichment <- function(total_background_hops, + total_experiment_hops, + background_hops, + experiment_hops, + pseudocount = 0.1) { + + # Input validation + if (!all(is.numeric(c(total_background_hops, total_experiment_hops, + background_hops, experiment_hops)))) { + stop("All inputs must be numeric") + } + + # Get the length of the region vectors + n_regions <- length(background_hops) + + # Ensure experiment_hops is same length as background_hops + if (length(experiment_hops) != n_regions) { + stop("background_hops and experiment_hops must be the same length") + } + + # Recycle scalar totals to match region length if needed + if (length(total_background_hops) == 1) { + total_background_hops <- rep(total_background_hops, n_regions) + } + if (length(total_experiment_hops) == 1) { + total_experiment_hops <- rep(total_experiment_hops, n_regions) + } + + # Now check all are same length + if (length(total_background_hops) != n_regions || + length(total_experiment_hops) != n_regions) { + stop("All input vectors must be the same length or scalars") + } + + # Calculate enrichment + numerator <- experiment_hops / total_experiment_hops + denominator <- (background_hops + pseudocount) / total_background_hops + enrichment <- numerator / denominator + + # Check for invalid values + if (any(enrichment < 0, na.rm = TRUE)) { + stop("Enrichment values must be non-negative") + } + if (any(is.na(enrichment))) { + stop("Enrichment values must not be NA") + } + if (any(is.infinite(enrichment))) { + stop("Enrichment values must not be infinite") + } + + return(enrichment) +} + + +#' Calculate Poisson p-values +#' +#' @param total_background_hops Total number of hops in background (scalar or vector) +#' @param total_experiment_hops Total number of hops in experiment (scalar or vector) +#' @param background_hops Number of hops in background per region (vector) +#' @param experiment_hops Number of hops in experiment per region (vector) +#' @param pseudocount Pseudocount for lambda calculation (default: 0.1) +#' @param ... additional arguments to `ppois`. note that lower tail is set to FALSE +#' already +#' @return Poisson p-values +calculate_poisson_pval <- function(total_background_hops, + total_experiment_hops, + background_hops, + experiment_hops, + pseudocount = 0.1, + ...) { + + # Input validation + if (!all(is.numeric(c(total_background_hops, total_experiment_hops, + background_hops, experiment_hops)))) { + stop("All inputs must be numeric") + } + + # Get the length of the region vectors + n_regions <- length(background_hops) + + # Ensure experiment_hops is same length as background_hops + if (length(experiment_hops) != n_regions) { + stop("background_hops and experiment_hops must be the same length") + } + + # Recycle scalar totals to match region length if needed + if (length(total_background_hops) == 1) { + total_background_hops <- rep(total_background_hops, n_regions) + } + if (length(total_experiment_hops) == 1) { + total_experiment_hops <- rep(total_experiment_hops, n_regions) + } + + # Now check all are same length + if (length(total_background_hops) != n_regions || + length(total_experiment_hops) != n_regions) { + stop("All input vectors must be the same length or scalars") + } + + # Calculate hop ratio + hop_ratio <- total_experiment_hops / total_background_hops + + # Calculate expected number of hops (mu/lambda parameter) + # Add pseudocount to avoid mu = 0 + mu <- (background_hops + pseudocount) * hop_ratio + + # Observed hops in experiment + x <- experiment_hops + + # Calculate p-value: P(X >= x) = 1 - P(X < x) = 1 - P(X <= x-1) + # This is equivalent to: 1 - CDF(x) + PMF(x) + # Using the upper tail directly with lower.tail = FALSE + pval <- ppois(x - 1, lambda = mu, lower.tail = FALSE, ...) + + return(pval) +} + + +#' Calculate hypergeometric p-values +#' +#' @param total_background_hops Total number of hops in background (scalar or vector) +#' @param total_experiment_hops Total number of hops in experiment (scalar or vector) +#' @param background_hops Number of hops in background per region (vector) +#' @param experiment_hops Number of hops in experiment per region (vector) +#' @param ... additional arguments to phyper. Note that lower tail is set to +#' false already +#' @return Hypergeometric p-values +calculate_hypergeom_pval <- function(total_background_hops, + total_experiment_hops, + background_hops, + experiment_hops, + ...) { + + # Input validation + if (!all(is.numeric(c(total_background_hops, total_experiment_hops, + background_hops, experiment_hops)))) { + stop("All inputs must be numeric") + } + + # Get the length of the region vectors + n_regions <- length(background_hops) + + # Ensure experiment_hops is same length as background_hops + if (length(experiment_hops) != n_regions) { + stop("background_hops and experiment_hops must be the same length") + } + + # Recycle scalar totals to match region length if needed + if (length(total_background_hops) == 1) { + total_background_hops <- rep(total_background_hops, n_regions) + } + if (length(total_experiment_hops) == 1) { + total_experiment_hops <- rep(total_experiment_hops, n_regions) + } + + # Now check all are same length + if (length(total_background_hops) != n_regions || + length(total_experiment_hops) != n_regions) { + stop("All input vectors must be the same length or scalars") + } + + # Hypergeometric parameters + # M: total number of balls (total hops) + M <- total_background_hops + total_experiment_hops + # n: number of white balls (experiment hops) + n <- total_experiment_hops + # N: number of draws (hops in region) + N <- background_hops + experiment_hops + # x: number of white balls drawn (experiment hops in region) - 1 for upper tail + x <- experiment_hops - 1 + + # Handle edge cases + valid <- (M >= 1) & (N >= 1) + pval <- rep(1, length(M)) + + # Calculate p-value for valid cases: P(X >= x) = 1 - P(X <= x-1) + if (any(valid)) { + pval[valid] <- phyper(x[valid], n[valid], M[valid] - n[valid], N[valid], + lower.tail = FALSE, ...) + } + + return(pval) +} + +# GRanges Conversion Functions -------------------------------------------- + +#' Convert BED format data frame to GRanges +#' +#' Handles coordinate system conversion from 0-indexed half-open BED format +#' to 1-indexed closed GenomicRanges format +#' +#' @param bed_df Data frame with chr, start, end columns in BED format (0-indexed, half-open) +#' @param zero_indexed Logical, whether input is 0-indexed (default: TRUE) +#' @return GRanges object +bed_to_granges <- function(bed_df, zero_indexed = TRUE) { + + if (!all(c("chr", "start", "end") %in% names(bed_df))) { + stop("bed_df must have columns: chr, start, end") + } + + # Convert from 0-indexed half-open [start, end) to 1-indexed closed [start, end] + if (zero_indexed) { + gr_start <- bed_df$start + 1 + gr_end <- bed_df$end + } else { + gr_start <- bed_df$start + gr_end <- bed_df$end + } + + # Create GRanges object (strand-agnostic for calling cards) + gr <- GRanges( + seqnames = bed_df$chr, + ranges = IRanges(start = gr_start, end = gr_end), + strand = "*" + ) + + # Add any additional metadata columns + extra_cols <- setdiff(names(bed_df), c("chr", "start", "end", "strand")) + if (length(extra_cols) > 0) { + mcols(gr) <- bed_df[, extra_cols, drop = FALSE] + } + + return(gr) +} + + +#' Deduplicate insertions in GRanges object +#' +#' For calling cards, if an insertion is found at the same coordinate, +#' only one record is retained +#' +#' @param gr GRanges object +#' @return Deduplicated GRanges object +deduplicate_granges <- function(gr) { + # Find unique ranges (ignores strand and metadata) + unique_ranges <- !duplicated(granges(gr)) + gr[unique_ranges] +} + + +#' Count overlaps between insertions and regions +#' +#' @param insertions_gr GRanges object with insertions +#' @param regions_gr GRanges object with regions +#' @param deduplicate Whether to deduplicate insertions (default: TRUE) +#' @return Integer vector of overlap counts per region +count_overlaps <- function(insertions_gr, regions_gr, deduplicate = TRUE) { + + # Deduplicate if requested + if (deduplicate) { + n_before <- length(insertions_gr) + insertions_gr <- deduplicate_granges(insertions_gr) + n_after <- length(insertions_gr) + if (n_before != n_after) { + message(" Deduplicated: ", n_before, " -> ", n_after, + " (removed ", n_before - n_after, " duplicates)") + } + } + + # Count overlaps per region + # countOverlaps returns an integer vector with one element per region + counts <- countOverlaps(regions_gr, insertions_gr) + + return(counts) +} + + +# Main Analysis Function -------------------------------------------------- + +#' Call peaks/quantify regions using calling cards approach +#' +#' @param experiment_gr GRanges object with experiment insertions +#' @param background_gr GRanges object with background insertions +#' @param regions_gr GRanges object with regions to quantify +#' @param deduplicate_experiment Whether to deduplicate experiment insertions (default: TRUE) +#' @param pseudocount Pseudocount for calculations (default: 0.1) +#' @return GRanges object with regions and statistics as metadata columns +enrichment_analysis <- function(experiment_gr, + background_gr, + regions_gr, + deduplicate_experiment = TRUE, + pseudocount = 0.1) { + + message("Starting enrichment analysis...") + + # Validate inputs + if (!inherits(experiment_gr, "GRanges")) { + stop("experiment_gr must be a GRanges object") + } + if (!inherits(background_gr, "GRanges")) { + stop("background_gr must be a GRanges object") + } + if (!inherits(regions_gr, "GRanges")) { + stop("regions_gr must be a GRanges object") + } + + # Count overlaps for experiment (with deduplication if requested) + message("Counting experiment overlaps...") + if (deduplicate_experiment) { + message(" Deduplication: ON") + } else { + message(" Deduplication: OFF") + } + + experiment_counts <- count_overlaps( + experiment_gr, regions_gr, + deduplicate = deduplicate_experiment + ) + + # Count overlaps for background (never deduplicated) + message("Counting background overlaps...") + message(" Deduplication: OFF (background should not be deduplicated)") + + background_counts <- count_overlaps( + background_gr, regions_gr, + deduplicate = FALSE + ) + + # Calculate total hops AFTER any deduplication + if (deduplicate_experiment) { + experiment_gr_dedup <- deduplicate_granges(experiment_gr) + total_experiment_hops <- length(experiment_gr_dedup) + } else { + total_experiment_hops <- length(experiment_gr) + } + + total_background_hops <- length(background_gr) + + message("Total experiment hops: ", total_experiment_hops) + message("Total background hops: ", total_background_hops) + + if (total_experiment_hops == 0) { + stop("Experiment data is empty") + } + if (total_background_hops == 0) { + stop("Background data is empty") + } + + # Add counts and totals as metadata columns + mcols(regions_gr)$experiment_hops <- as.integer(experiment_counts) + mcols(regions_gr)$background_hops <- as.integer(background_counts) + mcols(regions_gr)$total_experiment_hops <- as.integer(total_experiment_hops) + mcols(regions_gr)$total_background_hops <- as.integer(total_background_hops) + + # Calculate statistics + message("Calculating enrichment scores...") + mcols(regions_gr)$callingcards_enrichment <- calculate_enrichment( + total_background_hops = total_background_hops, + total_experiment_hops = total_experiment_hops, + background_hops = background_counts, + experiment_hops = experiment_counts, + pseudocount = pseudocount + ) + + message("Calculating Poisson p-values...") + mcols(regions_gr)$poisson_pval <- calculate_poisson_pval( + total_background_hops = total_background_hops, + total_experiment_hops = total_experiment_hops, + background_hops = background_counts, + experiment_hops = experiment_counts, + pseudocount = pseudocount + ) + + message("Calculating log Poisson p-values...") + mcols(regions_gr)$log_poisson_pval <- calculate_poisson_pval( + total_background_hops = total_background_hops, + total_experiment_hops = total_experiment_hops, + background_hops = background_counts, + experiment_hops = experiment_counts, + pseudocount = pseudocount, + log.p = TRUE + ) + + message("Calculating hypergeometric p-values...") + mcols(regions_gr)$hypergeometric_pval <- calculate_hypergeom_pval( + total_background_hops = total_background_hops, + total_experiment_hops = total_experiment_hops, + background_hops = background_counts, + experiment_hops = experiment_counts + ) + + message("Calculating log hypergeometric p-values...") + mcols(regions_gr)$log_hypergeometric_pval <- calculate_hypergeom_pval( + total_background_hops = total_background_hops, + total_experiment_hops = total_experiment_hops, + background_hops = background_counts, + experiment_hops = experiment_counts, + log.p = TRUE + ) + + # Calculate adjusted p-values + message("Calculating adjusted p-values...") + mcols(regions_gr)$poisson_qval <- p.adjust(mcols(regions_gr)$poisson_pval, method = "fdr") + mcols(regions_gr)$hypergeometric_qval <- p.adjust(mcols(regions_gr)$hypergeometric_pval, method = "fdr") + + message("Analysis complete!") + + return(regions_gr) +} + + +# Example Usage ----------------------------------------------------------- + +PROMOTERS = 'start_codon_500bp' + +genomic_features = arrow::read_parquet("~/code/hf/yeast_genome_resources/brentlab_features.parquet") + +genome_map_replicate_ds = arrow::open_dataset("~/code/hf/callingcards/genome_map", unify_schemas = TRUE) +genome_map_replicate_meta = arrow::read_parquet("~/code/hf/callingcards/genome_map_meta.parquet") + +background_gr <- read_tsv("~/code/hf/callingcards/adh1_background_ucsc.qbed") |> + mutate(id = "adh1_bg", + score = scales::rescale(depth, to = c(1,1000))) |> + dplyr::select(chr, start, end, id, score, strand) |> + bed_to_granges() + + +regions_list = list( + yiming = read_tsv("~/code/hf/yeast_genome_resources/yiming_promoters.bed", + col_names = c('chr', 'start', 'end', 'locus_tag', 'score', 'strand')) %>% + bed_to_granges(), + mindel = arrow::read_parquet("~/code/hf/yeast_genome_resources/mindel_promoters.parquet", + col_names = c('chr', 'start', 'end', 'locus_tag', 'score', 'strand')) %>% + bed_to_granges(), + start_codon_500bp = rtracklayer::import("~/code/hf/yeast_genome_resources/start_codon_500bp_upstream_promoters.bed"), + intergenic = rtracklayer::import("~/code/hf/yeast_genome_resources/intergenic_regions_5_1.bed") +) + +# rename name to target_locus_tag +colnames(GenomicRanges::mcols(regions_list$yiming))[1] <- "target_locus_tag" +colnames(GenomicRanges::mcols(regions_list$start_codon_500bp))[1] <- "target_locus_tag" + +intergenic_meta = read_csv("~/code/hf/yeast_genome_resources/intergenic_regions_metadata_5_1.csv") |> + dplyr::select(ir_name, chr, start, end, feature_left, feature_right) |> + pivot_longer(-c(ir_name, chr, start, end), names_to = 'side', values_to = 'target_locus_tag') |> + left_join(dplyr::select(genomic_features, target_locus_tag = locus_tag, + target_symbol = symbol, target_strand = strand, + target_start = start, target_end = end)) |> + filter(chr != "chrM") |> + filter(!is.na(target_strand)) |> + mutate(valid = (target_strand == '-' & target_end <= start) + | (target_strand == '+' & target_start >= end)) |> + filter(valid) + +regions_gr <- regions_list[[PROMOTERS]] + +# removes AAD6 and AAD16 from mindel. pseudogene no longer in annotations +if(PROMOTERS != "intergenic"){ + # really just for mindel + regions_gr = regions_gr[!is.na(regions_gr$target_locus_tag)] +} else if(PROMOTERS == "intergenic"){ + regions_gr = regions_gr[regions_gr$name %in% unique(intergenic_meta$ir_name)] +} +library(parallel) + +n_cores = 25 + + +results_replicates <- mclapply( + genome_map_replicate_meta$id, + \(x) enrichment_analysis( + experiment_gr = genome_map_replicate_ds |> + filter(id == x) |> + collect() |> + dplyr::rename(score = depth) |> + relocate(chr, start, end, id, score, strand) |> + mutate(depth = scales::rescale(score, to = c(1, 1000))) |> + bed_to_granges(), + background_gr = background_gr, + regions_gr = regions_gr, + deduplicate_experiment = TRUE, + pseudocount = 0.1 + ), + mc.cores = n_cores +) +names(results_replicates) = genome_map_replicate_meta$id + + +if(PROMOTERS == "intergenic"){ + + results_replicates_df = bind_rows(map(results_replicates, as_tibble), .id = "genome_map_id") |> + mutate(genome_map_id = as.integer(genome_map_id)) |> + dplyr::rename(ir_name = name) |> + left_join(dplyr::select(intergenic_meta, ir_name, target_locus_tag, target_symbol), + relationship = "many-to-many") |> + left_join(genome_map_replicate_meta, + by = c("genome_map_id" = "id")) |> + select(genome_map_id, batch, + target_locus_tag, target_symbol, ir_name, + experiment_hops, background_hops, + total_background_hops, total_experiment_hops, + callingcards_enrichment, + poisson_pval, log_poisson_pval, poisson_qval, + hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> + mutate(genome_map_id = as.integer(genome_map_id)) + + arrow::write_dataset( + results_replicates_df, + path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_intergenic", + format = "parquet", + partitioning = c("batch"), + existing_data_behavior = "overwrite", + compression = "zstd", + write_statistics = TRUE, + use_dictionary = c( + genome_map_id = TRUE + ) + ) + +} else if(PROMOTERS == "start_codon_500bp"){ + + +results_replicates_df = bind_rows(map(results_replicates, as_tibble), .id = "genome_map_id") |> + mutate(genome_map_id = as.integer(genome_map_id)) |> + left_join(dplyr::select(genomic_features, target_locus_tag = locus_tag, target_symbol = symbol)) |> + left_join(genome_map_replicate_meta, + by = c("genome_map_id" = "id")) |> + select(genome_map_id, batch, + target_locus_tag, target_symbol, + experiment_hops, background_hops, + total_background_hops, total_experiment_hops, + callingcards_enrichment, + poisson_pval, log_poisson_pval, poisson_qval, + hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> + mutate(genome_map_id = as.integer(genome_map_id)) + +arrow::write_dataset( + results_replicates_df, + path = "/home/chase/code/hf/callingcards/annotated_feature_reprocess_start_codon_500", + format = "parquet", + partitioning = c("batch"), + existing_data_behavior = "overwrite", + compression = "zstd", + write_statistics = TRUE, + use_dictionary = c( + genome_map_id = TRUE + ) + ) + +} + +# creating the combined data for a new set + +passing_rep_gm_ids <- unlist(strsplit(unique(arrow::read_parquet("~/code/hf/callingcards/2026_analysis_set.parquet")$gm_id), "-")) + +genome_map_replicate_meta_combined = genome_map_replicate_meta |> + filter(id %in% passing_rep_gm_ids) |> + group_by(regulator_locus_tag, regulator_symbol, condition) |> + mutate(id = as.character(id)) |> + reframe(combined_id = if (n() > 1) paste(id, collapse = "-") else id) + +# # Run analysis with deduplication (default for calling cards) +results_combined <- map(genome_map_replicate_meta_combined$combined_id, ~{ + # get list of ids (might just be 1) + ids <- as.integer(strsplit(.x, "-")[[1]]) + ids <- ids[!is.na(ids)] + + # for each id, produce a GRanges + combined_passing_set <- map(ids, ~{ + genome_map_replicate_ds |> + filter(id == .x) |> + collect() |> + dplyr::rename(score = depth) |> + relocate(chr, start, end, id, score, strand) |> + mutate(depth = scales::rescale(score, to = c(1, 1000))) |> + bed_to_granges() |> + deduplicate_granges() + }) + + # combine the list into a single gr + combined_gr <- do.call(c, combined_passing_set) + + enrichment_analysis( + experiment_gr = combined_gr, + background_gr = background_gr, + regions_gr = regions_gr, + deduplicate_experiment = FALSE, + pseudocount = 0.1 + ) +}) +names(results_combined) = genome_map_replicate_meta_combined$combined_id + +if(PROMOTERS == 'intergenic'){ + results_combined_analysis_df = bind_rows(map(results_combined, as_tibble), .id = "combined_id") |> + dplyr::rename(ir_name = name) |> + left_join(dplyr::select(intergenic_meta, ir_name, target_locus_tag, target_symbol), + relationship = "many-to-many") |> + left_join(genome_map_replicate_meta_combined) |> + select(combined_id, + regulator_locus_tag, regulator_symbol, condition, + target_locus_tag, target_symbol, experiment_hops, background_hops, + total_background_hops, total_experiment_hops, + callingcards_enrichment, + poisson_pval, log_poisson_pval, poisson_qval, + hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> + filter(condition == "standard") + + results_combined_analysis_df |> + ungroup() |> + dplyr::select(-condition) |> + arrange(regulator_locus_tag) |> + arrow::write_parquet( + "/home/chase/code/hf/callingcards/annotated_feature_reprocess_intergenic_analysis.parquet", + compression = "zstd", + write_statistics = TRUE, + use_dictionary = TRUE + ) + +} else if(PROMOTERS == "start_codon_500bp"){ + results_combined_analysis_df = bind_rows(map(results_combined, as_tibble), .id = "combined_id") |> + left_join(dplyr::select(genomic_features, target_locus_tag = locus_tag, target_symbol = symbol)) |> + left_join(genome_map_replicate_meta_combined) |> + select(combined_id, + regulator_locus_tag, regulator_symbol, condition, + target_locus_tag, target_symbol, experiment_hops, background_hops, + total_background_hops, total_experiment_hops, + callingcards_enrichment, + poisson_pval, log_poisson_pval, poisson_qval, + hypergeometric_pval, log_hypergeometric_pval, hypergeometric_qval) |> + filter(condition == "standard") + + results_combined_analysis_df |> + ungroup() |> + dplyr::select(-condition) |> + arrange(regulator_locus_tag) |> + arrow::write_parquet( + "/home/chase/code/hf/callingcards/annotated_feature_reprocess_start_codon_500bp_analysis.parquet", + compression = "zstd", + write_statistics = TRUE, + use_dictionary = TRUE + ) + +} +