cellSig: Hit identification

In OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

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"), ...)

## S4 method for signature 'cellData'
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"])

Example output

[1] "SigMat"    "threshold" "stats"     "pvalue"   

OperaMate documentation built on Nov. 17, 2017, 1:55 p.m.