WGCNA: goodGenes – R documentation

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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 and values whose weight is below a threshold: the fraction of missing values must be below a given threshold and the total number of present samples must be at least equal to a given threshold. If weights are given, entries whose relative weight is below a threshold will be considered missing.

Usage

goodGenes(
  datExpr, 
  weights = NULL,
  useSamples = NULL, 
  useGenes = NULL, 
  minFraction = 1/2, 
  minNSamples = ..minNSamples, 
  minNGenes = ..minNGenes, 
  tol = NULL,
  minRelativeWeight = 0.1,
  verbose = 1, indent = 0)

Arguments

`datExpr`	expression data. A data frame in which columns are genes and rows ar samples.
`weights`	optional observation weights in the same format (and dimensions) as `datExpr`.
`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.
`tol`	an optional 'small' number to compare the variance against. Defaults to the square of `1e-10 * max(abs(datExpr), na.rm = TRUE)`. The reason of comparing the variance to this number, rather than zero, is that the fast way of computing variance used by this function sometimes causes small numerical overflow errors which make variance of constant vectors slightly non-zero; comparing the variance to `tol` rather than zero prevents the retaining of such genes as 'good genes'.
`minRelativeWeight`	observations whose relative weight is below this threshold will be considered missing. Here relative weight is weight divided by the maximum weight in the column (gene).
`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.

Details

The constants ..minNSamples and ..minNGenes are both set to the value 4.

If weights are given, entries whose relative weight (i.e., weight divided by maximum weight in the column or gene) will be considered missing.

For most data sets, the fraction of missing samples criterion will be much more stringent than the absolute number of missing samples criterion.

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.

Author(s)

Peter Langfelder and Steve Horvath