OperaMate (version 1.4.0)

cellSig: Hit identification

Description

Detects samples those are most different from the negative controls.

Usage

cellSig(object, method = c("stable", "ksd", "kmsd"), th = NULL, thPval = 0.05, digits = 3, adjust.method = p.adjust.methods, plot = TRUE, outpath = getOption("opm.outpath"), ...)
"cellSig"(object, method = c("stable", "ksd", "kmsd"), th = NULL, thPval = 0.05, digits = 3, adjust.method = p.adjust.methods, plot = TRUE, outpath = getOption("opm.outpath"), ...)

Arguments

object

a cellData object

method

method = c("stable","ksd","kmsd"). Details are referred in the vignette.

th

numeric, the thresholds. It can be one threshold for both high and low expressed hit or two thresholds for each respectively.

thPval

numeric, threshold of pvalues in the t-test between the sample and control replicates

digits

integer, the number of digits used to show the thresholds

adjust.method

pvalue correction method

plot

plot QQ-plot when method is "stable" if TRUE.

outpath

directory of output figures, default: getOption("opm.outpath")

...

arguments of the graphic device

Value

a cellData object with initialized slot Sig.

Examples

data(demoCell)
op <- options("device")
options("device" = "png")
oneCell <- cellSig(oneCell, method = "stable", th = c(0.05, 0.05),
outpath = tempdir())
options(op)
names(oneCell["Sig"])