frip: Fraction of reads in peaks

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

Description

Calculate the FRiP metric (fraction of reads in peaks).

Usage

frip(reads, peaks, singleEnd = T)

Arguments

reads	File path, GRanges, GAlignments, GAlignmentPairs, BamViews or BamFile object containing reads from ChIP sample.
peaks	GRanges object indicating positions and widths of peaks or spp peaks as output by find.binding.positions or add.broad.peak.regions.
singleEnd	Only applicable when reads is a BamViews or BamFile object; set to TRUE for single-end data, FALSE for paired-end data.

Details

frip counts the number of mapped reads that fall into regions which were identified as binding positions (peaks) in a ChIP-Seq experiment. It returns the ratio [mapped reads in peaks] / [all mapped reads]. High values are an indicator of a good signal-to-noise ratio.

Note that the method used for peak identification influences the FRiP value. A comparison of FRiP values between experiments is only possible, if the same method was used for identifying peaks (i.e., same peak-caller with identical parameters).

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

Fraction of reads in peaks.

Examples

library(rtracklayer)
frip("chip.bam", import.bed("peaks.bed"))

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