Bioinformatics Toolbox™

genevarfilter - Filter genes with small profile variance

Syntax

Mask = genevarfilter(Data) [Mask, FData] = genevarfilter(Data) [Mask, FData, FNames] = genevarfilter(Data,Names) genevarfilter(..., 'PropertyName', PropertyValue,...) genevarfilter(..., 'Prctile', PrctileValue) genevarfilter(..., 'AbsValue', AbsValValue)

Arguments

`Data`	Matrix where each row corresponds to a gene. The first column is the names of the genes, and each additional column is the results from an 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.
`Prctile`	Property to specify a percentile below which gene expression profiles are removed. Enter a value from `0` to `100.`
`AbsValue`	Property to specify an absolute value below which gene expression profiles are removed.

Description

Gene profiling experiments have genes that exhibit little variation in the profile and are generally not of interest in the experiment. These genes are commonly removed from the data.

Mask = genevarfilter(Data) calculates the variance for each gene expression profile in Data and then identifies the expression profiles with a variance 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 than the threshold are 0.

[Mask, FData] = genevarfilter(Data) returns the filtered data matrix (FData). You can also create FData using FData = Data(find(I),:).

[Mask, FData, FNames] = genevarfilter(Data,Names) returns a filtered names array (FNames). Names is a cell array of the names of the genes corresponding to each row of Data. FNames can also be created using FNames = Names(I).

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

genevarfilter(..., 'Prctile', PrctileValue) removes from the experimental data (Data) gene expression profiles with a variance less than the percentile (Prctile).

genevarfilter(..., 'AbsValue', AbsValValue) removes from Data gene expression profiles with a variance less than AbsValue.

Examples

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

References