Extension of the GenomicRanges package

Description

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

• colnames returns the column name of a GRanges or GRangesList object.

• unsafeAppend appends two GAlignments object together bypassing most sanity checks. Faster than the standard c or append function.

Usage

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

Arguments

Details

• colnames returns the actual column names of the elementMetadata slot of the GRanges or GRangesList object. The elementMetadata contains a DataFrame object used to store additional information provided by the user, such as exon ID in our case.

• unsafeAppend appends two GAlignments objects.

Value

• colnames: A vector of column names.

• unsafeAppend: A GAlignments object

Author(s)

Nicolas Delhomme

See Also

• DataFrame

• GRanges

• GRangesList

• GAlignments row_colnames

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")
                          )

	# 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())