easyRNASeq GenomicRanges package extension {easyRNASeq}R Documentation

Extension of the GenomicRanges package

Description

Describes extensions to the GenomicRanges package. For GRanges and GRangesList objects:

Usage

colnames(x, do.NULL = TRUE, prefix = "col")
unsafeAppend(obj1,obj2)

Arguments

x

An object of the GRanges or GRangesList class

do.NULL

see row_colnames for details

prefix

see row_colnames for details

obj1

A GAlignments object

obj2

A GAlignments object

Details

Value

Author(s)

Nicolas Delhomme

See Also

Examples


 # an example of annotation
	grngs <- GRanges(seqnames=c("chr01","chr01","chr02"),
                     ranges=IRanges(
                             start=c(10,30,100),
                             end=c(21,53,123)),
                          strand=c("+","+","-"),
                          transcripts=c("trA1","trA2","trB"),
                          gene=c("gA","gA","gB"),
                          exon=c("e1","e2","e3")
                          )

	# accessing the colnames
	colnames(grngs)

	# creating a GRangesList
	grngsList<-split(grngs,seqnames(grngs))

	# accessing the colnames
	colnames(grngsList)

# For unsafeAppend
library(GenomicAlignments)
unsafeAppend(GAlignments(),GAlignments())


[Package easyRNASeq version 2.30.0 Index]