plotWhiskers {puma}R Documentation

Standard errors whiskers plot

Description

A plot showing error bars for genes of interest.

Usage

plotWhiskers(
        eset
,       comparisons=c(1,2)
,       sortMethod = c("logRatio", "PPLR")
,       numGenes=50
,       xlim
,       main = "PUMA Whiskers plot"
,       highlightedGenes=NULL
)

Arguments

eset An object of class ExpressionSet.
comparisons A 2-element integer vector specifying the columns of data to be compared.
sortMethod The method used to sort the genes. "logRatio" is fold change. PPLR is Probability of Positive Log Ratio (as determined by the pumaDE method).
numGenes Integer. Number of probesets to plot.
xlim The x limits of the plot. See plot.default.
main A main title for the plot. See plot.default.
highlightedGenes Row numbers of probesets to highlight with an asterisk.

Value

This function has no return value. The output is the plot created.

Author(s)

Richard D. Pearson

See Also

Related method pumaDE


[Package puma version 1.8.1 Index]