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WGCNA (version 1.25-1)

goodGenes: Filter genes with too many missing entries

Description

This function checks data for missing entries and returns a list of genes that have non-zero variance and pass two criteria on maximum number of missing values: the fraction of missing values must be below a given threshold and the total number of missing samples must be below a given threshold.

Usage

goodGenes(datExpr, 
          useSamples = NULL, 
          useGenes = NULL, 
          minFraction = 1/2, 
          minNSamples = ..minNSamples, 
          minNGenes = ..minNGenes, 
          verbose = 1, indent = 0)

Arguments

datExpr
expression data. A data frame in which columns are genes and rows ar samples.
useSamples
optional specifications of which samples to use for the check. Should be a logical vector; samples whose entries are FALSE will be ignored for the missing value counts. Defaults to using all samples.
useGenes
optional specifications of genes for which to perform the check. Should be a logical vector; genes whose entries are FALSE will be ignored. Defaults to using all genes.
minFraction
minimum fraction of non-missing samples for a gene to be considered good.
minNSamples
minimum number of non-missing samples for a gene to be considered good.
minNGenes
minimum number of good genes for the data set to be considered fit for analysis. If the actual number of good genes falls below this threshold, an error will be issued.
verbose
integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.
indent
indentation for diagnostic messages. Zero means no indentation, each unit adds two spaces.

Value

  • A logical vector with one entry per gene that is TRUE if the gene is considered good and FALSE otherwise. Note that all genes excluded by useGenes are automatically assigned FALSE.

Details

The constants ..minNSamples and ..minNGenes are both set to the value 4. For most data sets, the fraction of missing samples criterion will be much more stringent than the absolute number of missing samples criterion.

See Also

goodSamples, goodSamplesGenes