write.files {spliceSites} | R Documentation |
Writes table data and sequence in separate files.
write.files(x, path, filename,...)
x |
caRanges or aaGapSites object for which data is written. |
path |
Path for writing files. |
filename |
Basic filename to which suffixes are added. |
... |
Other arguments passed to "write.table". |
There are two files written: A text file with tabulated values from data.frame (separated by ";") and a fasta file which contains the stored dna sequence.
None.
The function tries to create directory 'path' when it does not exist.
Wolfgang Kaisers
# A) Read gap-sites from BAM-files bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) # B) Load DNA sequence dnafile<-system.file("extdata","dna_small.RData",package="spliceSites") load(dnafile) # C) Add DNA sequence lj<-lJunc(ga,featlen=21,gaplen=21,strand='+') ljc<-lCodons(lj,frame=1,keepStrand=TRUE) cdr<-dnaRanges(ljc,dna_small) # D) Translate DNA to amino-acid ar<-translate(cdr) # E) Write "ar.csv" and "ar.fa" # write.files(ar,".","ar")