ChromaBlocks: A function to find areas of enrichment in sequencing data
In Repitools: Epigenomic tools

Description Usage Arguments Value Author(s) See Also

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

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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)

`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