DBAmmd-Accessors: Extract data from DBAmmd objects

In dhelekal/mmdiff3: Statistical Testing for ChIP-Seq data sets

Description

This help file describes different ways to access the slots and values contained in a DBAmmd-class objects.

Usage

## S4 method for signature 'DBAmmd'
Genome(x)

## S4 method for signature 'DBAmmd'
Samples(x)

## S4 method for signature 'DBAmmd'
numPeaks(x)

## S4 method for signature 'DBAmmd'
numSamples(x)

## S4 method for signature 'DBAmmd'
metaData(x)

## S4 method for signature 'DBAmmd'
Regions(x)

## S4 method for signature 'DBAmmd'
Reads(x, whichPos = "Center")

## S4 method for signature 'DBAmmd'
Counts(x, whichCounts = "T")

## S4 method for signature 'DBAmmd'
Hists(x, whichPos = "Center")

## S4 method for signature 'DBAmmd'
Dists(x, dist.method = NULL)

## S4 method for signature 'DBAmmd'
Contrast(x, whichContrast = 1)

## S4 method for signature 'DBAmmd'
setRegions(x, Regions)

## S4 method for signature 'DBAmmd'
setContrast(x, contrast)

## S4 method for signature 'DBAmmd'
subSet(x, Peak.IDs)

Arguments

x	a DBAmmd Object. An empty instance can be created using DBAmmd(). (See DBAmmd-class for more details.)
whichPos	specifies which relative positions of mapped fragments should to be considered. Can be one of: 'Left.p', 'Right.p', 'Right.p' and 'Left.n': Start and end positions of fragments mapping to positive or negative strand, respectively ('Right.p' and 'Left.n' are not available for single-end reads). Additionally inferred positions: 'Center.n','Center.p','Center','Left','Right'. (DEFAULT: 'Center')
whichCounts	can be 'T': total counts, or 'p','n': counts of reads mapping to positive, negative strand, respectively.
dist.method	specify method used for distances between samples. Currently only Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) implemented. (DEFAULT: 'MMD')
whichContrast	index determining which of the set contrast should be used. (DEFAULT: 1)
Regions	GRanges Object specifying the Regions of Interesst / Peaks.
contrast	determines how to set a new contrast for differential analysis. A contrast can be automatically created either 'byCondition', or 'byTissue'. The Contrast can also be manually set (see vignette for details).
Peak.IDs	Highlight specific subset of peaks (DEFAULT: NULL)

Value

Genome(x) returns the name of the used genome version, if set in the metaData.

Samples(x) returns the information which was provided in the SampleSheet.csv to describe the data.

numPeaks(x) returns the number of Peaks / Regions of Interest that are associated with the DBAmmd object.

numSamples(x) returns the number of samples associated with the DBAmmd object.

metaData(x) returns the metaData associated with the DBAmmd object.

Regions(x) returns the Peaks / Regions of Interest that are associated with the DBAmmd object.

Reads(x,whichPos) returns the Reads mapping to the Regions of Interest.

Counts(x,whichCounts) returns a m x n matrix containing the Counts of Reads mapping to the Peaks / Regions of Interest. Depending on the value of 'whichCounts', total counts ('T'), or counts of reads mapping to positive ('p'), or negative strand ('n') are returnt. See getPeakReads for more details.

Hists(x,whichPos) returns a list of matrices of length m (number of Peaks). Each matrix is a n x L_i matrix, where n is the number of samples and L_i is the number of bins used to cover the extend of the peak. Note, L_i varies between peaks of different lengths. See compHists for more details.

Dists(x,dist.method) returns a matrix containing distances between pairs of samples for each peak. See compDists for more details.

Contrast(x,whichContrast) returns the specified contrast.

setRegions(x,Regions) returns a DBAmmd Object with set Peaks / Regions of Interests.

setContrast(x,contrast) returns a DBAmmd Object with a set contrast.

setSet(x,idx) returns a DBAmmd Object with a subset of peak regions.

See Also

DBAmmd-class

Examples

data("MMD")

Samples(MMD)
Genome(MMD)
numPeaks(MMD)
numSamples(MMD)
metaData(MMD)
R <- Regions(MMD)
Pos <- Reads(MMD)
C <- Counts(MMD)
H <- Hists(MMD)
D <- Dists(MMD)
C1 <- Contrast(MMD)

dhelekal/mmdiff3 documentation built on July 25, 2019, 8:18 p.m.