| Bioinformatics Toolbox | |
Filter genes with small profile variance
Mask = genevarfilter(Data,
'PropertyName', PropertyValue...)
[Mask, FData] = genevarfilter(Data)
[Mask, FData, FNames] = genevarfilter(Data, Names)
genevarfilter(..., 'Prctile', PrctileValue)
genevarfilter(..., 'AbsValue', AbsValueValue)
Data | Matrix where each row corresponds to a gene. The first column is the name of the genes, and each additional column is the results from an experiment. |
Names | Cell array with the same number of rows as Data. Each row contains 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. |
Gene profiling experiments have genes which exhibit little variation in the profile and are generally not of interest in the experiment. Removing (filtering) these genes from the data is a commonly done.
Mask = genevarfilter(Data, 'PropertyName', PropertyValue...) 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 then the threshold have a value of 1, and those with a variance less then the threshold are 0.
[Mask, FData] = genevarfilter(Data) returns the filtered data matrix FData. FData can also be created 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(..., 'Prctile', PrctileValue) removes from 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.
load yeastdata [fyeastvalues, fgenes] = genevarfilter(yeastvalues,genes);
Bioinformatics Toolbox functions exprprofrange, exprprofvar, generangefilter
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