ChromaBlocks {Repitools} | R Documentation

## 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`

[Package Repitools version 1.28.0 Index]