annoByGtfchipseq.Rd
This function executes the docker container annotate.1, where refGenome is used to annotated gene.results and isoforms.results outputs from RSEM using ENSEMBL GTF annotation
annoByGtfchipseq( group = "docker", peaks.file = getwd(), gtf.file, extension = 10000 )
group, | a character string. Two options: |
---|---|
peaks.file, | a character string indicating the MACS peak file, extension _peaks.xls, with full path |
gtf.file, | a character string indicating the file, with full path for the genome gtf |
extension, | a number defining how many nucleotides should be expandend the extremes of the targetr gene to find an overlap with peaks, default 10000 |
one file: MACS2 peaks annotated
if (FALSE) { #downloading fastq files #running rsemannoByGtfchipseq annoByGtfchipseq(group="docker", peaks.file=paste(getwd(),"h3k9me1_igg_peaks.xls", sep="/"), gtf.file=paste("/Users/raffaelecalogero/Dropbox/courses/DUKENUS_JUL2019/course/course/datasets/genomes/mm10bwa","Mus_musculus.GRCm38.97.gtf", sep="/"), extension=10000) }