calcRP_coverage {FindIT2} | R Documentation |
calculate regulatory potential using big wig files, which is useful for ATAC or H3K27ac histone modification data.
calcRP_coverage( bwFile, Txdb, gene_included, Chrs_included, decay_dist = 1000, scan_dist = 20000, verbose = TRUE )
bwFile |
bw file |
Txdb |
Txdb |
gene_included |
a character vector which represent gene set which you want to calculate RP for |
Chrs_included |
a character vector which represent chromosomes where you want to calculate gene RP in |
decay_dist |
decay distance |
scan_dist |
scan distance |
verbose |
whether you want to report detailed running message |
Please note that because of rtracklayer::import has some issue on 32 bit R of windows, so the calcRP_coverage can not work on this system. But if your R is 64 bit, which now be applied on the most windows R, this function still work.
data.frame
if (.Platform$OS.type != "windows" & require(TxDb.Athaliana.BioMart.plantsmart28)) { Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) bwFile <- system.file("extdata", "E50h_sampleChr5.bw", package = "FindIT2") RP_df <- calcRP_coverage( bwFile = bwFile, Txdb = Txdb, Chrs_included = "Chr5" ) }