dba.analyze: Perform differential binding affinity analysis

Description

Performs differential binding affinity analysis

Usage

dba.analyze(DBA, method=DBA$config$AnalysisMethod,  bSubControl=TRUE, bFullLibrarySize=TRUE, bTagwise=TRUE, bCorPlot=DBA$config$bCorPlot,   bReduceObjects=T,  bParallel=DBA$config$RunParallel)

Arguments

DBA

DBA object. If no contrasts are specified (DBA$contrast is NULL), default contrasts will be added via a call to dba.contrast.

method

method, or vector of methods, by which to analyze differential binding affinity. Supported methods:

also, for backward compatibility:

DBA_DESEQ

Additionally, if this value is set to DBA_ALL_METHODS, this is equivalent to specifying c(DBA_EDGER,DBA_DESEQ2).

bSubControl

logical indicating whether Control read counts are subtracted for each site in each sample before performing analysis.

bFullLibrarySize

logical indicating if the full library size (total number of reads in BAM/SAM/BED file) for each sample is used for scaling normalization. If FALSE, the total number of reads present in the peaks for each sample is used (generally preferable if overall biding levels are expected to be similar between samples).

bTagwise

logical indicating if dispersion should be calculated on a tagwise (or per-condition) basis. If there are only a very few members of each group in a contrast (e.g. no replicates), this should be set to FALSE.

bCorPlot

logical indicating whether to plot a correlation heatmap for the analyzed data (first contrast only). If no sites are significantly differentially bound using the default threholds, no heatmap will be plotted.

bReduceObjects

logical indicating whether strip the analysis objects of unnecessary fields to save memory. If it is desired to used the DBA$contrasts[[n]]$edgeR and/or DBA$contrasts[[n]]$DESeq objects directly in the edgeR and/or DESeq packages, this should be set to FALSE.

bParallel

logical indicating that the analyses is to be done in parallel using multicore (one process for each contrast for each method, plus an additional process per method).

Value

DBA object with results of analysis added to DBA$contrasts.

Details

See the DBA User Guide for more details on how the edgeR and DESeq2 analyses are carried out.

Examples

Run this code

data(tamoxifen_counts)

tamoxifen <- dba.analyze(tamoxifen)
tamoxifen

data(tamoxifen_counts)
tamoxifen <- dba.contrast(tamoxifen,categories=DBA_CONDITION,block=tamoxifen$masks$MCF7)
tamoxifen <- dba.analyze(tamoxifen,method=DBA_ALL_METHODS)
tamoxifen