segReads-class: Classes and functions to segment the genome in candidate...
In PICS: Probabilistic inference of ChIP-seq

Description Usage Arguments Functions Note

Pre-process bidirectional aligned reads data from a single ChIP-Seq experiment to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by PICS.

segReads(yF, yR, cF, cR, map, chr)

segReadsList(List, paraSW, N, Nc)

## S4 method for signature 'segReads'
show(object)

## S4 method for signature 'segReadsList'
show(object)

map(x, ...)

## S4 method for signature 'segReads'
map(x)

## S4 method for signature 'segReadsList'
map(x)

## S4 method for signature 'segReadsList'
length(x)

## S4 method for signature 'segReadsList'
summary(object)

## S4 method for signature 'segReads'
summary(object)

## S4 method for signature 'segReadsList,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'segReadsList,ANY,ANY'
x[[i, j, ..., exact = TRUE]]

`yF`	A `numeric` vector. Forward reads.
`yR`	A `numeric` vector. Reverse reads.
`cF`	A `numeric` vector. Forward reads for the controls.
`cR`	A `numeric` vector. Reverse reads for the controls.
`map`	A `matrix`. The mappability profile.
`chr`	A `character`. Chromosome name.
`List`	A `list` of `segReads` objects.
`paraSW`	A `list` of parameters for the genomic regions.
`N`	A `numeric`. The number of reads in the data.
`Nc`	A `numeric`. The number of reads in the control.
`object, x`	A `segReads` object.
`i, j, ..., exact, drop`	Additional arguments passed to subset methods.

segReads: segReads Constructor
segReadsList: segReadsList Constructor
show,segReads-method: show method
show,segReadsList-method: show method
map: map generic
map,segReads-method: map method
map,segReadsList-method: map method
length,segReadsList-method: Return length of segReadsList
summary,segReadsList-method: Summary method
summary,segReads-method: Summary method
[,segReadsList,ANY,ANY,ANY-method: Subset methods
[[,segReadsList,ANY,ANY-method: Subset methods