getIntrons_byGenes: Get introns by genes

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

Get introns by genes

Usage

getIntrons_byGenes(txdb, seqout = "DESeq_outputs/XR1_annotated.out",
  padjFilter = 0.05, genome_mart = "hsapiens_gene_ensembl", outfile)

Arguments

txdb	A TxDb object
seqout	The annotated DESeq Output
padjFilter	p-value cutoff
genome_mart	the name of mart object to annotate the input with (eg : hsapiens_gene_ensembl)
outfile	output file with introns, to write back

Value

annotated DESeq output with introns for each gene

Examples

## Not run: 
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
deout <- system.file("extdata", "edgeR_output_annotated.tsv", package="vivlib")
getIntrons_byGenes(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene, seqout = deout,
padjFilter = 0.05, genome_mart = "hsapiens_gene_ensembl", outfile = "annotated_introns.out")

## End(Not run)

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.