IDRfilter {ChIPpeakAnno} | R Documentation |
Using IDR to assess the consistency of replicate experiments and obtain a high-confidence single set of peaks
IDRfilter( peaksA, peaksB, bamfileA, bamfileB, maxgap = -1L, minoverlap = 0L, singleEnd = TRUE, IDRcutoff = 0.01, ... )
peaksA, peaksB |
peaklist, GRanges object. |
bamfileA, bamfileB |
file path of bam files. |
maxgap, minoverlap |
Used in the internal call to |
singleEnd |
(Default TRUE) A logical indicating if reads are single or paired-end. |
IDRcutoff |
If the IDR no less than IDRcutoff, the peak will be removed. |
... |
Not used. |
An object GRanges
Jianhong Ou
Li, Qunhua, et al. "Measuring reproducibility of high-throughput experiments." The annals of applied statistics (2011): 1752-1779.
if(interactive()){ path <- system.file("extdata", "reads", package="MMDiffBamSubset") if(file.exists(path)){ bamfileA <- file.path(path, "reads", "WT_2.bam") bamfileB <- file.path(path, "reads", "Resc_2.bam") WT.AB2.Peaks <- file.path(path, "peaks", "WT_2_Macs_peaks.xls") Resc.AB2.Peaks <- file.path(path, "peaks", "Resc_2_Macs_peaks.xls") peaksA=toGRanges(WT.AB2.Peaks, format="MACS") peaksB=toGRanges(Resc.AB2.Peaks, format="MACS") library(idr) library(DelayedArray) IDRfilter(peaksA, peaksB, bamfileA, bamfileB) } }