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
)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

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

Value

one file: MACS2 peaks annotated

Author

Raffaele Calogero

Examples

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)
}