getSelfConsistencyRatios: Get self-consistency ratios

In imbforge/encodeChIPqc: A set of useful ChIPseq QC metrics from the ENCODE project

Description

Calculate the ratio of peaks below a given IDR threshold between all pseudo-replicates

Usage

getSelfConsistencyRatios(chipTuples, idrCutoff = 0.01)

Arguments

chipTuples	output of calculateIDR
idrCutoff	count only peaks below this IDR value (for mammalian cells a value of 0.01 is recommended)

Details

The ChIP-Seq guidelines of the ENCODE consortium recommend that the number of peaks with an IDR below 0.01 should not differ by more than a factor of 2 between any pair of pseudo-replicates. This function counts the peaks of all pseudo-replicates with an IDR <= 0.01 and calculates the quotient of the number of peaks for all possible pairs of pseudo-replicates. It produces a N x N matrix, where N is the number of true replicates. The values of the matrix are calculated as:

[peak count of replicate in column] / [peak count of replicate in row]

All values should be within a range of 0.5 to 2. Deviations from this range indicate low reproducibility.

Ref: Stephen G. Landt, Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, Peter Bickel, James B. Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles Epstein, Katherine I. Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J. Hartemink, Michael M. Hoffman, Vishwanath R. Iyer, Youngsook L. Jung, Subhradip Karmakar, Manolis Kellis, Peter V. Kharchenko, Qunhua Li, Tao Liu, X. Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, Richard M. Myers, Peter J. Park, Michael J. Pazin, Marc D. Perry, Debasish Raha, Timothy E. Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, John A. Stamatoyannopoulos, Michael Y. Tolstorukov, Kevin P. White, Simon Xi, Peggy J. Farnham, Jason D. Lieb, Barbara J. Wold, Michael Snyder: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Genome Res. Sep 2012; 22(9): 1813<e2><80><93>1831.

Value

matrix with quotients of peak counts for all possible combinations of replicates

Examples

chipTuples <- calculateIDR(c("IP1.bam", "IP2.bam"), c("input1.bam", "input2.bam"),
                            "Hsapiens", "UCSC", "hg19")
getSelfConsistencyRatios(chipTuples)

imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.