Package 'WGCNA' - Laboratory Web Sites - UCLA

48 goodSamples
Usage
goodSamples(datExpr,
useSamples = NULL,
useGenes = NULL,
minFraction = 1/2,
minNSamples = ..minNSamples,
minNGenes = ..minNGenes,
verbose = 1, indent = 0)
Arguments
datExpr
useSamples
useGenes
minFraction
minNSamples
minNGenes
verbose
indent
expression data. A data frame in which columns are genes and rows ar samples.
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.
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.
minimum fraction of non-missing samples for a gene to be considered good.
minimum number of good samples for the data set to be considered fit for analysis.
If the actual number of good samples falls below this threshold, an error
will be issued.
minimum number of non-missing samples for a sample to be considered good.
integer level of verbosity. Zero means silent, higher values make the output
progressively more and more verbose.
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. 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 sample that is TRUE if the sample is considered good and FALSE
otherwise. Note that all samples excluded by useSamples are automatically assigned FALSE.
Author(s)
Peter Langfelder and Steve Horvath
See Also
goodSamples, goodSamplesGenes