## ----eval = FALSE------------------------------------------------------------- # # import bed file # genelist <- import.bed("~/data/genelists/genes.bed") # # # import gff # genelist <- import.gff("~/data/genelists/genes.gff") # # # export a bed file after modifying # export.bed(genelist, "~/data/genelists/filtered_genes.bed") ## ----message = FALSE---------------------------------------------------------- library(BRGenomics) ## ----------------------------------------------------------------------------- data("txs_dm6_chr4") tx4 <- txs_dm6_chr4[c(1, 10, 200, 300)] tx4 ## ----------------------------------------------------------------------------- tx4_pr <- promoters(tx4, upstream = 50, downstream = 100) tx4_pr width(tx4_pr) ## ----------------------------------------------------------------------------- tx4 ## ----------------------------------------------------------------------------- genebodies(tx4, start = 300, end = -300) ## ----------------------------------------------------------------------------- genebodies(tx4, -50, 100, fix.end = "start") ## ----------------------------------------------------------------------------- genebodies(tx4, -100, -50, fix.end = "start") ## ----------------------------------------------------------------------------- genebodies(tx4, -1000, 1000, fix.start = "end") ## ----------------------------------------------------------------------------- genebodies(tx4, 0, 10000, fix.start = "end") ## ----------------------------------------------------------------------------- txs <- txs_dm6_chr4[order(txs_dm6_chr4$gene_id)] # sort by gene_id txs[1:10] ## ----------------------------------------------------------------------------- reduceByGene(txs, gene_names = txs$gene_id) ## ----------------------------------------------------------------------------- txs_redux <- reduceByGene(txs, gene_names = txs$gene_id) txs_redux$gene_id <- names(txs_redux) names(txs_redux) <- NULL txs_redux ## ----------------------------------------------------------------------------- txs[1:10] txs_insxt <- intersectByGene(txs, gene_names = txs$gene_id) txs_insxt[order(names(txs_insxt))]