mm_geneBound {FindIT2} | R Documentation |
find related peaks of your input genes, which is useful when you want to plot volcano plot or heatmap of peaks.
mm_geneBound(peak_GR, Txdb, input_genes, verbose = TRUE, ...)
peak_GR |
peak GRange with a column named feature_id representing you peak name |
Txdb |
Txdb |
input_genes |
a character vector which represent genes set which you want to find related peak for |
verbose |
whether you want to report detailed running message |
... |
additional arguments in distanceToNearest |
data.frame with three column: related peak id, your input gene id, and distance
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) peak_pair <- mm_geneBound(peak_GR, Txdb, c("AT5G01015", "AT5G67570")) peak_pair }