segReads-class: Classes and functions to segment the genome in candidate...

Description Usage Arguments Functions Note

Description

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.

Usage

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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]]

Arguments

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.

Functions

Note

segReads and segReadsList objects are not meant to be built via the constructors. The constructors are used in segmentPICS.


SRenan/PICS documentation built on Jan. 19, 2020, 5:59 a.m.