getAssocPairNumber {FindIT2} | R Documentation |
get associated peak number of gene and vice verse.
getAssocPairNumber( mmAnno, output_type = c("gene_id", "feature_id"), output_summary = FALSE )
mmAnno |
the annotated GRange object from mm_geneScan or mm_nearestGene |
output_type |
one of 'gene_id' or 'feature_id' |
output_summary |
whether you want to detailed info |
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) peakAnno <- mm_nearestGene(peak_GR, Txdb) getAssocPairNumber(peakAnno) }