Bioinformatics Toolbox™

geneentropyfilter - Remove genes with low entropy expression values

Syntax

Mask = geneentropyfilter(Data) [Masks, FData] = geneentropyfilter(Data) [Mask, FData, FNames] = geneentropyfilter(Data,Names) geneentropyfilter(..., 'PropertyName', PropertyValue,...) geneentropyfilter(..., 'Percentile', PercentileValue)

Arguments

`Data`	Matrix where each row corresponds to the experimental results for one gene. Each column is the results for all genes from one experiment.
`Names`	Cell array with the name of a gene for each row of experimental data. `Names` has same number of rows as `Data` with each row containing the name or ID of the gene in the data set.
`PercentileValue`	Property to specify a percentile below which gene data is removed. Enter a value from `0` to `100`.

Description

Mask = geneentropyfilter(Data) identifies gene expression profiles in Data with entropy values less than the 10th percentile.

Mask is a logical vector with one element for each row in Data. The elements of Mask corresponding to rows with a variance greater than the threshold have a value of 1, and those with a variance less then the threshold are 0.

[Masks, FData] = geneentropyfilter(Data) returns a filtered data matrix (FData). FData can also be created using FData = Data(find(I),:).

[Mask, FData, FNames] = geneentropyfilter(Data,Names) returns a filtered names array (FNames). You can also create FNames using FNames = Names(I).

geneentropyfilter(..., 'PropertyName', PropertyValue,...) defines optional properties using property name/value pairs.

geneentropyfilter(..., 'Percentile', PercentileValue) removes from the experimental data (Data) gene expression profiles with entropy values less than a given percentile (PercentileValue).

Examples

load yeastdata
[fyeastvalues, fgenes] = geneentropyfilter(yeastvalues,genes);

References