Filter expression data

Description

This function takes an expression matrix and filtered out non detected genes.

Usage

1
expFilter(data, threshold = 3.5, p=0.01, graph = TRUE)

Arguments

data

expression matrix, genes on rows and samples on columns.

threshold

minimal value of expression to be reached

p

keep probes with at least p*ncol(data) samples higher than threshold

graph

boolean indicating if an histogram of the data should be plotted.

...

Arguments to be passed to methods, such as graphical parameters (see 'par').

Details

The non variant genes are defined gy the threshold value. A gene is kept if at least p*ncol(data) of its values is higher than threshold.

The graph represents the distribution of all the genes in Data. A line shows the threshold value used.

Value

An expression matrix.

Author(s)

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe

Examples

1
2
data(marty)
expFilter(marty, threshold = 3.5, graph = TRUE)

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