easyRNASeq GenomicRanges package extension

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Extension of the GenomicRanges package

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.

Keywords
methods
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
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.

Value

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

See Also

  • DataFrame
  • GRanges
  • GRangesList
  • GAlignmentscolnames

Aliases
  • colnames
  • colnames,GRanges-method
  • colnames,GRangesList-method
  • easyRNASeq GenomicRanges package extension
  • unsafeAppend
  • unsafeAppend,GAlignments,GAlignments-method
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())
Documentation reproduced from package easyRNASeq, version 2.8.2, License: Artistic-2.0

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