dba.plotVolcano: Generate volcano plots of differential binding analysis...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/DBA.R

Description

Generates volcano plots of differential binding analysis results.

Usage

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dba.plotVolcano(DBA, contrast=1, method=DBA$config$AnalysisMethod, 
                            th=DBA$config$th, bUsePval=DBA$config$bUsePval, 
                            fold=0, factor="", bFlip=FALSE, 
                            bLabels=FALSE, maxLabels=50, dotSize=1)

Arguments

DBA

DBA object, on which dba.analyze should have been successfully run.

contrast

number of contrast to report on. See dba.show(DBA, bContrast=TRUE) to get contrast numbers.

method

method or vector of methods to plot results for:

  • DBA_DESEQ2

  • DBA_DESEQ2_BLOCK

  • DBA_EDGER

  • DBA_EDGER_BLOCK

th

significance threshold; sites with FDR (or p-values, see bUsePval) less than or equal to this value will be colored red in the plot

bUsePval

logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.

fold

will only include sites with fold change greater than this as significant (colored red).

factor

string to be prepended to plot main title; e.g. factor name.

bFlip

logical indicating that order of groups in contrast should be "flipped", allowing control of which sample group will have positive and which will have negative fold changes.

bLabels

logical indicating that labels should be drawn on the plot. The labels are the site numbers, the row index in the (silently) returned set of significant sites. The maximim number of sites can be specified using maxLabels.

maxLabels

The maximum number of labels to use in the plot. Ignored if bLabels=FALSE.

dotSize

size of points on plot.

Details

Makes a volcal plot.

Value

silently returns a GRanges object of the sites higlighted in red.

Author(s)

Rory Stark

See Also

dba.analyze, dba.plotMA

Examples

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data(tamoxifen_analysis)

# default volcano plot
dba.plotVolcano(tamoxifen)

# only highlight significant sites with at least 10x Fold Change
sigSites <- dba.plotVolcano(tamoxifen, fold=log2(10))

# use labels to find outlier sites
sigSites <- dba.plotVolcano(tamoxifen, fold=5,bLabels=TRUE)
sigSites

DiffBind documentation built on Jan. 11, 2018, 2 a.m.