calcRP_TFHit {FindIT2} | R Documentation |
calculate regulatory potential based on ChIP-Seq peak data, which is useful for TF ChIP-seq data.
calcRP_TFHit( mmAnno, Txdb, decay_dist = 1000, report_fullInfo = FALSE, verbose = TRUE )
mmAnno |
the annotated GRange object from mm_geneScan |
Txdb |
Txdb |
decay_dist |
decay distance |
report_fullInfo |
whether you want to report full peak-RP-gene info |
verbose |
whether you want to report detailed running message |
If your origin peak_GR of mmAnno have column named feature_score, calcRP_TFHit will consider this column when calculating sumRP. Otherwise, it will consider all peak Hit feature_score is 1.
if report_fullInfo is TRUE, it will output GRanges with detailed info. While FALSE, it will output data frame
if (require(TxDb.Athaliana.BioMart.plantsmart28)){ Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2") peak_GR <- loadPeakFile(peak_path) mmAnno <- mm_geneScan(peak_GR, Txdb) # if you just want to get RP_df, you can set report_fullInfo FALSE fullRP_hit <- calcRP_TFHit( mmAnno = mmAnno, Txdb = Txdb, report_fullInfo = TRUE ) RP_df <- metadata(fullRP_hit)$peakRP_gene }