getRatio: Building ratio over experiments

In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description

This function calculates the ratio over experiments.

Usage

getRatio(eSet, ip, control, description, fkt=median, featureData=F) 

Arguments

eSet	An ExpressionSet, containing the logged raw intensities
ip	a boolean or integer vector, that indicate, which columns in the matrix are IP experiments
control	a boolean or integer vector, that indicate, which columns in the matrix are CONTROL or REFERENCE experiments
description	description of the new data (e.g. IPvsCONTROL)
fkt	mean or median to calculate the averaged intensity over replicates
featureData	if TRUE, featureData is added to the new ExpressionSet

Author(s)

Benedikt Zacher [e-mail]

Examples

##
# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
# 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
# names <- c("rpb3_1", "wt_1","rpb3_2")
# type <- c("IP", "CONTROL", "IP")
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)

# ips <- rpb3Chr1$type == "IP"
# controls <- rpb3Chr1$type == "CONTROL"

# rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")
# description <- c("Rpb3vsWT")
# rpb3_rankpercentile_ratio <- getRatio(rpb3_rankpercentile, ips, controls, description, fkt=median, featureData=FALSE)

Starr documentation built on April 28, 2020, 7:52 p.m.