exportTargetGenes: Function to export sorted RBP target genes

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Function to export sorted RBP target genes

Description

Genes with binding sites are target genes of the RBP. They can be exported as 'csv' or 'xlsx' file. Genes can be sorted by the sum of the individual binding sites score, or by the number of binding sites per gene.

Usage

exportTargetGenes(
  object,
  path = "./",
  format = c("csv", "xslx"),
  sort = c("score", "bs"),
  split = c("none", "geneType", "transcriptRegion")
)

Arguments

object	a BSFDataSet object with stored ranges
path	A path to where the output should be stored
format	output file format
sort	sorting rule for genes
split	if and how the output file should be split

Details

As output option, one can either output all genes in a single file, or split by either gene-type or transcript-region. This options requires that either BSFind or the individual functions assignToGenes, and assignToTranscriptRegions were run.

Value

a file of the type specified in format

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
## Not run: 
# export
# exportTargetGenes(bds)

## End(Not run)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.