marker: Reference signal

In alexandremkuhn/PSEA: Population-Specific Expression Analysis.

Description

Generates a population-specific reference signal.

Usage

marker(expr,id,sampleSubset=NULL,targetMean=1)

Arguments

expr	Numeric matrix or ExpressionSet. The matrix contains the expression data with transcripts (i.e. for a microarray, probes) as rows and samples as columns. Row names should be defined and are used to determine the transcripts used to generate the reference signal (specified with the argument id). If an ExpressionSet is provided the expression data is extracted with the function exprs.
id	List of strings. Names of the transcripts to use to generate the reference signal. Names correspond to row names in expr if it is a matrix or row names in exprs(expr) if it is an ExpressionSet).
sampleSubset	Integer vector. Represents a subset of samples (specified as column indices in expr) to use to normalize the reference signal (see Details). By default all samples are used.
targetMean	Numeric. Mean of the reference signal (defaults to 1).

Details

A reference signal for a given population is generated by averaging the expression of multiple transcripts that are expressed in a cell population-specific manner.

The reference signal is scaled to have an average value determined by targetMean (1 by default). The argument sampleSubset restricts the samples to take into account for normalization (i.e. the average of the reference signal over sampleSubset will be the value specified by targetMean, but the reference signal will still be of length equal to the number of columns in expr).

The expression value of each transcript is normalized before averaging over multiple transcripts so that they have same weight in the final reference signal (i.e to avoid that highly expressed transcripts dominate the reference signal).

The names of transcripts to be used are specified as items of a list (id). If the expression matrix contains multiple measures of the same transcript (for instance several probes of a microarray measuring the same transcript) they can be averaged before taking the average over different transcripts. Thereby every transcript has the same weight in the final reference signal, independently of the number of probes used to measure it. Multiple measures of the same transcript are specified as a vector in the list.

Value

refSignal

Numeric vector of the same length as the number of columns in expr (or in exprs(expr) if expr is provided as an ExpressionSet). Reference signal (see Details).

Author(s)

Alexandre Kuhn [e-mail]

References

Kuhn A, Thu D, Waldvogel HJ, Faull RL, Luthi-Carter R. Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain. Nat Methods 2011, 8(11):945-7

Examples

## Load example expression data
data("example")

## List of probes corresponding to neuronal genes:
## 221805_at, 221801_x_at, 221916_at all measure NEFL expression.
## 201313_at, 210040_at, 205737_at, 210432_s_at measure
## ENO2, SLC12A5, KCNQ2 and SCN3A expression, respectively.
neuron_probesets <- list(c("221805_at", "221801_x_at", "221916_at"),
		"201313_at", "210040_at", "205737_at", "210432_s_at")

## Neuronal reference signal
neuron_reference <- marker(expression, neuron_probesets)

alexandremkuhn/PSEA documentation built on March 26, 2020, 12:04 a.m.