GenomicRanges-methods: Extension of the GenomicRanges package
In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1 2	colnames(x, do.NULL = TRUE, prefix = "col") unsafeAppend(obj1,obj2)

`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

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.

colnames: A vector of column names.
unsafeAppend: A GAlignments object

Nicolas Delhomme

DataFrame
GRanges
GRangesList
GAlignments row_colnames

 # 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())