A function to find areas of enrichment in sequencing data

Description

This function discovers regions of enrichment in ChIP-seq data, using the method described in Hawkins RD. et al 2010 Cell Stem Cell.

Usage

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## S4 method for signature 'GRangesList,GRangesList'
ChromaBlocks(rs.ip, rs.input, organism, chrs, ipWidth=100, inputWidth=500, preset=NULL, blockWidth=NULL, minBlocks=NULL, extend=NULL, cutoff=NULL, FDR=0.01, nPermutations=5, nCutoffs=20, cutoffQuantile=0.98, verbose=TRUE, seq.len=NULL)

Arguments

rs.ip

A GRangesList object containing reads from the Immunoprecipited sample. If multiple lanes are supplied, they are pooled.

rs.input

A GRangesList object containing reads from the Input (unenriched) sample. If multiple lanes are supplied, they are pooled.

organism

The BSgenome object

chrs

An character or integer vector with the indicies of the chromosomes of the organism object to analyse

ipWidth

Size in basepairs of the windows to use for the IP samples

inputWidth

Size in basepairs of the windows to use for the Input samples

preset

Either "small", "large" to use cutoffs described in Hawkins et al or NULL (where blockWidth, minBlocks must be specified)

blockWidth

Number of adjacent blocks to consider at once

minBlocks

The minimum number of blocks required above cutoff

extend

Optional: whether to extend significant blocks until adjacent blocks are less than this value

cutoff

Optional: the cutoff to use to call regions. If left as NULL a cutoff will be chosen which satisfied the specified FDR

FDR

The target False Discovery Rate; If cutoff is not supplied, one will be chosen to satisfy this value

nPermutations

The number of permutations of the data to determine the cutoff at the supplied FDR

nCutoffs

The number of different cutoffs to try to satisfy the FDR, a higher value will give finer resolution but longer processing time

cutoffQuantile

The quantile of the RPKM to use as the maximum cutoff tried; a higher value will give lower resolution but may be needed if a cutoff satisfying the FDR cannot be determined with the default value

verbose

logical, whether to output commments of the processing

seq.len

If sequencing reads need to be extended, the fragment size to be used

Value

A ChromaResults object.

Author(s)

Aaron Statham

See Also

ChromaResults

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