get.z.matrix: Get z matrix

In emreg00/pepper: PErsonalized Perturbation ProfilER

Description

Returns z-score matrix for a given GEO data set. The z-scores are calculated for each gene in each sample using the mean and sd over provided control samples.

Usage

get.z.matrix(expr, sample.mapping, states.control = NULL,
  states.case = NULL, method = "mean", out.file = NULL)

Arguments

expr	Expression matrix (genes vs samples), tab separated.
sample.mapping	Sample - condition mapping.
states.control	Label of control (background) samples. If NULL sample.mapping is assumed to include the following types: "case" "control".
states.case	Label of case (disease) samples.
method	Method to calculate the z score, defaults to mean and sd, use median for med and mad.
out.file	Output file for writing z score matrix.

Value

Data frame containing z-scores

Examples

gds.data = fetch.expression.data("GDS4966", do.log2=F, probe.conversion="Gene ID")
expr = gds.data$expr
sample.mapping = gds.data$sample.mapping
z = get.z.matrix(expr, sample.mapping, 
	states.control = c("healthy donor"), 
	states.case = c("tuberculosis", "latent tuberculosis infection"))

emreg00/pepper documentation built on May 16, 2019, 5:10 a.m.