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| library(tidyverse) |
| library(janitor) |
| library(GenomicRanges) |
| library(here) |
|
|
| brentlab_features <- read_csv("~/projects/huggingface/yeast_genome_resources/brentlab_features.csv.gz") |
| intergenic_meta <- read_csv("~/projects/huggingface/yeast_genome_resources/intergenic_regions_metadata_5_1.csv") |
|
|
| promoters <- list( |
| bp500 = rtracklayer::import("~/projects/huggingface/yeast_genome_resources/start_codon_500bp_upstream_promoters.bed"), |
| mindel = GenomicRanges::GRanges(read_csv("~/projects/huggingface/yeast_genome_resources/mindel_promoters.csv.gz")), |
| kang = rtracklayer::import("~/projects/huggingface/yeast_genome_resources/yiming_promoters.bed"), |
| intergenic = rtracklayer::import("~/projects/huggingface/yeast_genome_resources/intergenic_regions_5_1.bed") |
| ) |
|
|
| GenomicRanges::mcols(promoters$mindel) <- GenomicRanges::mcols(promoters$mindel) |> |
| as.data.frame() |> |
| dplyr::transmute(name = target_locus_tag) |> |
| S4Vectors::DataFrame() |
|
|
|
|
| read_in_annotated_peaks <- function(peak_path) { |
| read_tsv(peak_path, |
| comment = "#", |
| col_names = c( |
| "chr", "start", "end", |
| "name", "score", "strand" |
| ) |
| ) |
| } |
|
|
| score_targets_replicates <- function(regulator, peaks_list, promoters_gr, score_thresh = -log10(0.1)) { |
| |
| matched <- peaks_list[str_detect(names(peaks_list), paste0("^", regulator))] |
|
|
| if (length(matched) == 0) { |
| warning(sprintf("No replicates found for regulator: %s", regulator)) |
| return(NULL) |
| } |
|
|
| bind_rows(matched, .id = "sample_id") |> |
| mutate(replicate = str_extract(sample_id, "[^_]+$")) |> |
| filter(score > score_thresh) |> |
| annotate_bed_peaks_to_promoters(promoters_gr) |> |
| group_by(promoter_id) |> |
| reframe( |
| n_replicates = n_distinct(replicate), |
| n_peaks = n(), |
| nearest_score = score[which.min(distance_to_tss)], |
| median_score = median(score), |
| max_score = max(score) |
| ) |
| } |
|
|
| annotate_bed_peaks_to_promoters <- function(peaks_df, promoters_gr) { |
| peaks_gr <- GenomicRanges::GRanges( |
| seqnames = peaks_df$chr, |
| ranges = IRanges::IRanges(start = peaks_df$start, end = peaks_df$end) |
| ) |
|
|
| hits <- GenomicRanges::findOverlaps(peaks_gr, promoters_gr, ignore.strand = TRUE) |
|
|
| if (length(hits) == 0) { |
| return(peaks_df |> dplyr::slice(0) |> dplyr::mutate(promoter_id = character(), distance_to_tss = numeric())) |
| } |
|
|
| promoter_strand <- as.character(GenomicRanges::strand(promoters_gr)) |
| promoter_start <- GenomicRanges::start(promoters_gr) |
| promoter_end <- GenomicRanges::end(promoters_gr) |
| promoter_name <- promoters_gr$name |
|
|
| peaks_df[S4Vectors::queryHits(hits), ] |> |
| dplyr::mutate( |
| promoter_id = promoter_name[S4Vectors::subjectHits(hits)], |
| .promoter_strand = promoter_strand[S4Vectors::subjectHits(hits)], |
| .promoter_start = promoter_start[S4Vectors::subjectHits(hits)], |
| .promoter_end = promoter_end[S4Vectors::subjectHits(hits)], |
| .peak_mid = (start + end) / 2, |
| .tss_pos = dplyr::if_else(.promoter_strand == "+", .promoter_end, .promoter_start), |
| distance_to_tss = abs(.peak_mid - .tss_pos) |
| ) |> |
| dplyr::select(-dplyr::starts_with(".")) |
| } |
|
|
| annotated_peaks <- list( |
| files = list.files(here("data/reprocessed_mahendrawada_results/peaks"), |
| "_peaks.bed", |
| full.names = TRUE, |
| recursive = TRUE |
| ) |
| ) |
| names(annotated_peaks$files) <- str_remove( |
| basename(annotated_peaks$files), |
| "_peaks.bed" |
| ) |
|
|
| annotated_peaks$df <- map(annotated_peaks$files, read_in_annotated_peaks) |
|
|
| regulators <- unique(str_remove(names(annotated_peaks$df), "_[A,B,C]$")) |
|
|
| target_scores <- list() |
| for (pset in names(promoters)) { |
| target_scores[[pset]] <- list() |
|
|
| for (r in regulators) { |
| rdf <- |
| score_targets_replicates( |
| regulator = r, |
| peaks_list = annotated_peaks$df, |
| promoters_gr = promoters[[pset]] |
| ) |
|
|
| if (pset == "intergenic") { |
| rdf <- rdf |> |
| left_join(intergenic_meta |> |
| dplyr::select( |
| promoter_id = ir_name, |
| feature_left, |
| feature_right |
| ) |> |
| pivot_longer(-promoter_id, values_to = "target_locus_tag") |> |
| dplyr::select(-name), relationship = "many-to-many") |> |
| dplyr::select(-promoter_id) |> |
| mutate(promoter_id = target_locus_tag) |> |
| dplyr::select(-target_locus_tag) |
| } |
|
|
| target_scores[[pset]][[r]] <- rdf |
| } |
| } |
|
|
| reformat_tmp <- function(df) { |
| df |> |
| separate_wider_delim(tmp, |
| delim = "x", names = c( |
| "regulator_symbol", |
| "condition" |
| ), |
| too_few = "align_start" |
| ) |> |
| mutate(target_locus_tag = promoter_id) |> |
| dplyr::select(-promoter_id) |> |
| left_join(dplyr::select(brentlab_features, |
| regulator_symbol = symbol, |
| regulator_locus_tag = locus_tag |
| )) |> |
| left_join(dplyr::select(brentlab_features, |
| target_locus_tag = locus_tag, |
| target_symbol = symbol |
| )) |> |
| dplyr::relocate(regulator_locus_tag, regulator_symbol, condition, target_locus_tag, target_symbol) |> |
| group_by(regulator_locus_tag, condition) |> |
| arrange(desc(max_score)) |> |
| ungroup() |> |
| filter( |
| !is.na(target_locus_tag), |
| !is.na(target_symbol) |
| ) |
| } |
|
|
| gm_meta <- arrow::read_parquet("~/projects/huggingface/mahendrawada_2025/chec_genome_map_meta.parquet") |
|
|
| target_scores_df <- purrr::map( |
| target_scores, |
| ~ dplyr::bind_rows(.x, .id = "tmp") |
| ) |> |
| dplyr::bind_rows(.id = "promoter_set") |> |
| reformat_tmp() |> |
| left_join( |
| gm_meta |> |
| dplyr::select(sample_id, regulator_locus_tag, condition) |> |
| distinct() |
| ) |> |
| dplyr::relocate(sample_id) |
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