MotifScan.RdScan gene promoters for a set of TF PWMs
MotifScan(seurat_obj, species_genome, pfm, EnsDb, wgcna_name = NULL)MotifScan
#> function (seurat_obj, species_genome, pfm, EnsDb, wgcna_name = NULL)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> motif_df <- data.frame(motif_name = purrr::map(1:length(pfm),
#> function(i) {
#> pfm[[i]]@name
#> }) %>% unlist, motif_ID = purrr::map(1:length(pfm), function(i) {
#> pfm[[i]]@ID
#> }) %>% unlist)
#> gene.promoters <- ensembldb::promoters(EnsDb)
#> gene.coords <- ensembldb::genes(EnsDb)
#> gene.promoters <- gene.promoters[gene.promoters$tx_biotype ==
#> "protein_coding"]
#> gene.coords <- gene.coords[gene.coords$gene_biotype == "protein_coding"]
#> gene.promoters <- gene.promoters[as.character(GenomeInfoDb::seqnames(gene.promoters)) %in%
#> c(1:100, "X", "Y")]
#> gene.coords <- gene.coords[as.character(GenomeInfoDb::seqnames(gene.coords)) %in%
#> c(1:100, "X", "Y")]
#> gene.promoters$symbol <- gene.coords$symbol[base::match(gene.promoters$gene_id,
#> names(gene.coords))]
#> gene.promoters <- GenomeInfoDb::keepSeqlevels(gene.promoters,
#> value = levels(droplevels(GenomeInfoDb::seqnames(gene.promoters))))
#> old_levels <- levels(GenomeInfoDb::seqnames(gene.promoters))
#> new_levels <- paste0("chr", old_levels)
#> gene.promoters <- GenomeInfoDb::renameSeqlevels(gene.promoters,
#> new_levels)
#> GenomeInfoDb::genome(GenomeInfoDb::seqinfo(gene.promoters)) <- species_genome
#> my_promoters <- GRanges(seqnames = droplevels(GenomeInfoDb::seqnames(gene.promoters)),
#> IRanges(start = start(gene.promoters), end = end(gene.promoters)),
#> symbol = gene.promoters$symbol, genome = species_genome)
#> print("Matching motifs...")
#> motif_ix <- motifmatchr::matchMotifs(pfm, my_promoters, genome = species_genome)
#> tf_match <- motifmatchr::motifMatches(motif_ix)
#> rownames(tf_match) <- my_promoters$symbol
#> colnames(tf_match) <- motif_df$motif_name
#> gene_list <- rownames(seurat_obj)
#> gene_list <- gene_list[gene_list %in% rownames(tf_match)]
#> tf_match <- tf_match[gene_list, ]
#> print("Getting putative TF target genes...")
#> tfs <- motif_df$motif_name
#> tf_targets <- list()
#> n_targets <- list()
#> for (cur_tf in tfs) {
#> tf_targets[[cur_tf]] <- names(tf_match[, cur_tf][tf_match[,
#> cur_tf]])
#> n_targets[[cur_tf]] <- length(tf_targets[[cur_tf]])
#> }
#> n_targets <- unlist(n_targets)
#> motif_df$n_targets <- n_targets
#> seurat_obj <- SetMotifMatrix(seurat_obj, tf_match)
#> seurat_obj <- SetMotifs(seurat_obj, motif_df)
#> seurat_obj <- SetMotifTargets(seurat_obj, tf_targets)
#> seurat_obj <- SetPFMList(seurat_obj, pfm)
#> seurat_obj
#> }
#> <bytecode: 0x7f77b99fac78>
#> <environment: namespace:hdWGCNA>