fig.CAT: Concordance At The Top Plot

In LXQin/PRECISION.seq: Comparison of Depth Normalization Methods

Description

Function for generating a concordance at the top plot, which compares concordance of the p-values of differential expression — typically from the normalized or raw data set data.test — to the p-values of differential expression of a gold standard — typically the data set data.benchmark.

Usage

fig.CAT(DEA, truth.DEA, title, maxrank = 100, subset = NULL)

Arguments

DEA	Results of a differential expression analysis using the included methods DE.voom or DE.edgeR. Must be a list including id.list List of differentially expressed markers p.val p-values for differential expression
truth.DEA	Gold standard (assumed truth) for differential expression. Must be in the same format as DEA.
title	optional Figure title
maxrank	optional specify the maximum size of top-ranked items that you want to plot.
subset	optional vector of a subset of genes/markers for this analysis

Value

figure of concordance for comparison

Examples

voom.benchmark <- DE.voom(data.benchmark, data.group)
test.norm <- pip.norm(raw=data.test, groups=data.group, norm.method = "all")
test.DE <- list(
TMM = DE.voom(RC=test.norm$TMM$dat.normed, groups = data.group),
TC = DE.voom(RC=test.norm$TC$dat.normed, groups = data.group),
UQ = DE.voom(RC=test.norm$UQ$dat.normed, groups = data.group),
med = DE.voom(RC=test.norm$med$dat.normed, groups = data.group),
DESeq = DE.voom(RC=test.norm$DESeq$dat.normed, groups = data.group),
PoissonSeq = DE.voom(RC=test.norm$PoissonSeq$dat.normed, groups = data.group),
QN = DE.voom(RC=test.norm$QN$dat.normed, groups = data.group),
RUVg = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVg$adjust.factor),
RUVs = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVs$adjust.factor),
RUVr = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVr$adjust.factor),
SVA = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$SVA$adjust.factor),
noNorm = DE.voom(RC=data.test, groups = data.group))

fig.CAT(DEA = test.DE, truth.DEA = voom.benchmark, title = "Example of CAT plot")

LXQin/PRECISION.seq documentation built on Dec. 18, 2021, 3:41 a.m.