Nothing
## ---- 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))]
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