dba.plotVolcano: Generate volcano plots of differential binding analysis...
In DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data

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

Generates volcano plots of differential binding analysis results.

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)

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 maximum 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.

Makes a volcano plot.

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

Rory Stark

dba.analyze, dba.plotMA

data(tamoxifen_analysis)

# default volcano plot
dba.plotVolcano(tamoxifen)

# only highlight significant sites with at least 5x Fold Change
sigSites <- dba.plotVolcano(tamoxifen, fold=log2(5))

# use labels to find outlier sites
sigSites <- dba.plotVolcano(tamoxifen, fold=log2(10),bLabels=TRUE)
sigSites