mm_geneScan {FindIT2} | R Documentation |
Annotate peaks using geneScan mode, which means every peak have more than one related genes.
mm_geneScan( peak_GR, Txdb, upstream = 3000, downstream = 3000, reportGeneInfo = FALSE, verbose = TRUE, ... )
peak_GR |
peak GRange with a column named feature_id representing you peak name |
Txdb |
Txdb |
upstream |
distance to start site(upstream) |
downstream |
distance to start site(downstream) |
reportGeneInfo |
whether you want to add gene info |
verbose |
whether you want to report detailed running message |
... |
additional arguments in findOverlaps |
Granges object with annotated info
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) peakAnno <- mm_geneScan(peak_GR, Txdb) peakAnno }