easyRNASeq GenomicRanges package extension {easyRNASeq} | R Documentation |
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.
colnames(x, do.NULL = TRUE, prefix = "col") unsafeAppend(obj1,obj2)
x |
An object of the |
do.NULL |
see |
prefix |
see |
obj1 |
A |
obj2 |
A |
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
# 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())