Usage
"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