Volcano.Anal: Volcano

In flajole/MApckg: R package of MetaboAnalyst functions

Description

The volcano plot is a combination of fold change and t-tests. Note, for unpaired samples, the x-axis is log (FC). For paired analysis, the x-axis is number of significant counts. Y-axis is -log10(p.value) for both cases. Writes an output file "volcano.csv"

Usage

Volcano.Anal(dataSet, analSet, paired = FALSE, fcthresh = 2, cmpType = 0,
  percent.thresh = 0.75, nonpar = FALSE, thresh = 0.05,
  var.equal = TRUE)

Arguments

dataSet	List, data set object generated by MS_to_MA function.
analSet	List, containing the results of statistical analysis (can be just an empty list).
paired	Are values in data set paired or not.
fcthresh	Fold-change threshold.
cmpType	Comparison type. If equal 0 then group 1 is compared against group 2. Otherwise, vice versa.
percent.thresh	Sig. count threshold (for paired data).
nonpar	If FALSE - use classical t-test; if TRUE - Wilcoxon Rank Test
thresh	Threshold of significance.
var.equal	Are variances assumed equal or not.

Value

Native analSet with one added $volcano element consisting of:

• $raw.threshx - value of fcthresh argument

• $raw.threshy - value of thresh argument

• $paired - -log10(thresh)

• $max.xthresh - upper log-threshold of fold change

• $min.xthresh - lower log-threshold of fold change

• $thresh.y - -log10(thresh)

• $fc.all - fold changes of all features

• $fc.log - log of fold changes

• $fc.log.uniq - java-object

• $inx.up - logical vector of increasing features

• $inx.down - logical vector of decreasing features

• $p.log - -log10(p.value)

• $inx.p - logical vector of features with p <= thresh

• $sig.mat - data frame of significant features

See Also

PlotVolcano for plotting functions

flajole/MApckg documentation built on May 16, 2019, 1:16 p.m.