Usage
diffExp(arrayData, contrasts, chromosomeMapping, fitMethod = "ls", adjustMethod = "fdr", significance = 0.001, plot = TRUE, heatmapCutoff = 1e-10, volcanoFC = 2, colors=c("red","green","blue","yellow", "orange","purple","tan","cyan","gray60","black"), save = FALSE, verbose = TRUE)
Arguments
arrayData
an object of class ArrayData
.
contrasts
a character vector giving the contrasts to be tested for differential expression.
Use extractFactors
to get allowed contrasts.
chromosomeMapping
character string giving the name of the chromosome mapping file, or an object of
class data.frame
or similar containing the chromosome mapping. Required for
the Polar plot if the ArrayData
object lacks annotation information. See
details below.
fitMethod
character string giving the fitting method used by lmFit
. Can be either
"ls"
for least squares (default) or "robust"
for robust regression.
adjustMethod
character string giving the method to use for adjustment of multiple testing.
Can be "holm"
, "hochberg"
, "hommel"
, "bonferroni"
,
"BH"
, "BY"
, "fdr"
(default) or "none"
. See p.adjust
for details.
significance
number giving the significance cutoff level for the Venn diagram and the horizontal line drawn in the volcano plot.
Defaults to 0.001
.
plot
should plots be produced? Set either to TRUE
(default) or FALSE
to control all plots, or to a character vector with any combination of "venn"
, "heatmap"
, "polarplot"
and "volcano"
, to control the single plots (e.g. plot=c("venn","polarplot")
or plot="heatmap"
).
heatmapCutoff
number giving the significance cutoff level for the heatmap. Defaults to
1e-10
.
volcanoFC
number giving the x-coordinates of the vertical lines drawn in the volcano plot. Defaults to
2
.
colors
character vector of colors to be used by the Venn diagram and Polar plot.
save
should the figures and p-values be saved? Defaults to FALSE
.
verbose
verbose? Defaults to TRUE
.