Description Usage Arguments Value Examples
This function extracts transcript information from the annotation file corresponding to reference genome
1 | transcriptExtract(annotationFile, databaseName, outputfile)
|
annotationFile |
The annotation file (in gtf, gff or gff3 fromat) corresponding to the reference genome |
databaseName |
The database name from where the annotation file was downloaded (the possible options are "ncbi", "ucsc" and "other") |
outputfile |
The name of the output file |
The transcript information from the annotation file will be written in the output file 'outputfile'
1 2 3 4 5 6 7 8 9 10 11 12 13 | #Loading an example annotation file and write to a file
#Here temporary directory is created as input-output
#directory. Please provide your own directory instead.
out_dir<-tempdir()
annotation_file<-data(refGenchr1)
annotation_file<-refGenchr1
write.table(annotation_file, file.path(out_dir,"annotation_file.gtf"),
row.names=FALSE, sep="\t",quote=FALSE, col.names=FALSE)
#Extraction of transcript information. Here, the output will be generated in file
#transcriptdata.txt in out_dir directory
transcriptExtract(file.path(out_dir,"annotation_file.gtf"), "ucsc",
file.path(out_dir, "transcriptdata.txt"))
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