goodSamplesGenes: Iterative filtering of samples and genes with too many...

Description Usage Arguments Details Value Author(s) See Also

View source: R/Functions.R

Description

This function checks data for missing entries and zero-variance genes, and returns a list of samples and genes that pass criteria maximum number of missing values. If necessary, the filtering is iterated.

Usage

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goodSamplesGenes(
  datExpr, 
  minFraction = 1/2, 
  minNSamples = ..minNSamples, 
  minNGenes = ..minNGenes, 
  tol = NULL,
  verbose = 1, indent = 0)

Arguments

datExpr

expression data. A data frame in which columns are genes and rows ar samples.

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'.

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

This function iteratively identifies samples and genes with too many missing entries and genes with zero variance. Iterations may be required since excluding samples effectively changes criteria on genes and vice versa. The process is repeated until the lists of good samples and genes are stable. The constants ..minNSamples and ..minNGenes are both set to the value 4.

Value

A list with the foolowing components:

goodSamples

A logical vector with one entry per sample that is TRUE if the sample is considered good and FALSE otherwise.

goodGenes

A logical vector with one entry per gene that is TRUE if the gene is considered good and FALSE otherwise.

Author(s)

Peter Langfelder

See Also

goodSamples, goodGenes


WGCNA documentation built on Aug. 5, 2017, 5:05 p.m.