ChromaBlocks: A function to find areas of enrichment in sequencing data

In markrobinsonuzh/Repitools: Epigenomic tools

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

## 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

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.