MGFM (version 1.6.0)

getMarkerGenes: Marker Gene Detection

Description

Function to detect marker genes using microarray gene expression data sets

Usage

getMarkerGenes(data.mat, samples2compare="all", annotate=TRUE, chip=NULL,
score.cutoff=1)

Arguments

data.mat

The microarray data matrix with probe sets corresponding to rows and samples corresponding to columns.

samples2compare

A character vector with the sample names to be compared (e.g. c("liver", "lung", "brain")). By default all samples are used.

annotate

A boolean value. If TRUE the gene symbol and the entrez gene id are shown.

chip

Chip name.

score.cutoff

A value in the interval [0,1] to filter the markers according to the specificity score. The default value is 1 (no filtering).

Value

A list with marker genes associated with each sample type.

Details

For each marker in the output list, the probe set and the corresponding score are shown. If annotate is TRUE, the gene symbol and the entrez gene id are shown. The score is used to rank the markers according to their specificity. The score values range from 0 to 1. Values near 0 would indicate high specificity and large values closer to 1 would indicate low specificity.

Examples

data("ds2.mat")
res.list <- getMarkerGenes(ds2.mat, samples2compare="all", annotate=TRUE,
chip="hgu133a", score.cutoff=1)
names(res.list)
## show the first 20 markers of liver
res.list[["liver_markers"]][1:20]