enhancerPromoterCor {FindIT2} | R Documentation |
enhancerPromoterCor
enhancerPromoterCor( peak_GR, Txdb, up_scanPromoter = 500, down_scanPromoter = 500, up_scanEnhancer = 20000, down_scanEnhacner = 20000, peakScoreMt, parallel = FALSE, verbose = TRUE )
peak_GR |
peak GRange with a column named feature_id representing you peak name |
Txdb |
Txdb |
up_scanPromoter |
the scan distance which is used to scan nearest promoter |
down_scanPromoter |
the scan distance which is used to scan nearest promoter |
up_scanEnhancer |
the scan distance which is used to scan feature |
down_scanEnhacner |
the scan distance which is used to scan feature |
peakScoreMt |
peak count matrix. The rownames are feature_id in peak_GR |
parallel |
whether you want to parallel to speed up |
verbose |
whether you want to report detailed running message |
mmAnno with Cor, pvalue,padj,qvalue column
if (require(TxDb.Athaliana.BioMart.plantsmart28)){ data("ATAC_normCount") Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2") peak_GR <- loadPeakFile(peak_path)[1:100] mm_ePLink <- enhancerPromoterCor( peak_GR = peak_GR, Txdb = Txdb, peakScoreMt = ATAC_normCount, parallel = FALSE) }