dnaRanges {spliceSites} | R Documentation |
bamReader
, refGenome
and gene name.Locates gene in genome via refGenome
and reads a bamRange
from the determined region.
dnaRanges(x,dnaset,useStrand=TRUE,removeUnknownStrand=TRUE,verbose=TRUE,...)
x |
cRanges. Range-data will be copied from this object. |
dnaset |
DNAStringSet. Contains the reference sequence from which the DNA-sequence is extracted. |
useStrand |
logical. When TRUE, sequences for which strand='-' are reverse-complemented. |
removeUnknownStrand |
logical. When TRUE, sequences for which strand='-' are removed. |
verbose |
logical. Determines amount of console output during routine runtime. |
... |
Optional additional arguments (currently unused). |
cdRanges
Wolfgang Kaisers
bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) lj<-lJunc(ga,featlen=6,gaplen=6,strand='+') dnafile<-system.file("extdata","dna_small.RData",package="spliceSites") load(dnafile) ljd<-dnaRanges(lj,dna_small) seqlogo(ljd)