easyRNASeq (version 2.8.2)

easyRNASeq GenomicRanges package extension: Extension of the GenomicRanges package

Description

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

• colnamesreturns the column name of aGRangesorGRangesListobject.
• unsafeAppendappends twoGAlignmentsobject together bypassing most sanity checks. Faster than the standardcorappendfunction.

Usage

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

Arguments

x

An object of the GRanges or GRangesList class

do.NULL

see colnames for details

prefix

see colnames for details

obj1

A GAlignments object

obj2

A GAlignments object

Value

• • colnames: A vector of column names.
  • unsafeAppend: AGAlignmentsobject

Details

• colnamesreturns the actual column names of the elementMetadata slot of theGRangesorGRangesListobject. The elementMetadata contains aDataFrameobject used to store additional information provided by the user, such as exon ID in our case.
• unsafeAppendappends twoGAlignmentsobjects.

See Also

• DataFrame
• GRanges
• GRangesList
• GAlignmentscolnames

Examples

## an example of a RangedData annotation
	gAnnot <- RangedData(
                     IRanges(
                             start=c(10,30,100),
                             end=c(21,53,123)),
                          space=c("chr01","chr01","chr02"),
                          strand=c("+","+","-"),
                          transcripts=c("trA1","trA2","trB"),
                          gene=c("gA","gA","gB"),
                          exon=c("e1","e2","e3"),
                          universe = "Hs19"
                          )

	## an example of a GRangesList annotation
	grngs <- as(gAnnot,"GRanges")

	## 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())