SharedJunc {customProDB} | R Documentation |
Load multiple BED files and output a GRange object with junctions present in multiple samples.
SharedJunc(juns, share_num = 2, ...)
juns |
a list of GRanges object which input from multiple VCF files using function InputVcf. |
share_num |
Junctions must occurs in this number of samples to be consider. Two options, percentage format or sample number. |
... |
additional arguments |
This function allows to limit junctions that are present in at least m out of n BED files.
a GRange object that contains the shared junctions
Xiaojing Wang
path <- system.file("extdata/beds", package="customProDB") bedFiles<- paste(path, '/', list.files(path, pattern="*bed$"), sep='') juncs <- lapply(bedFiles, function(x) Bed2Range(x, skip=1, covfilter=5)) shared <- SharedJunc(juncs, share_num=2) shared