Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
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42 goodGenesMS<br />
goodGenesMS<br />
Filter genes with too many missing entries across multiple sets<br />
Description<br />
This function checks data for missing entries and returns a list of genes that have non-zero variance<br />
in all sets and pass two criteria on maximum number of missing values in each given set: the fraction<br />
of missing values must be below a given threshold and the total number of missing samples must<br />
be below a given threshold<br />
Usage<br />
goodGenesMS(multiExpr,<br />
useSamples = NULL,<br />
useGenes = NULL,<br />
minFraction = 1/2,<br />
minNSamples = ..minNSamples,<br />
minNGenes = ..minNGenes,<br />
verbose = 1, indent = 0)<br />
Arguments<br />
multiExpr<br />
useSamples<br />
useGenes<br />
minFraction<br />
minNSamples<br />
minNGenes<br />
verbose<br />
indent<br />
expression data in the multi-set format (see checkSets). A vector of lists, one<br />
per set. Each set must contain a component data that contains the expression<br />
data, with rows corresponding to samples and columns to genes or probes.<br />
optional specifications of which samples to use for the check. Should be a logical<br />
vector; samples whose entries are FALSE will be ignored for the missing<br />
value counts. Defaults to using all samples.<br />
optional specifications of genes for which to perform the check. Should be a<br />
logical vector; genes whose entries are FALSE will be ignored. Defaults to<br />
using all genes.<br />
minimum fraction of non-missing samples for a gene to be considered good.<br />
minimum number of non-missing samples for a gene to be considered good.<br />
minimum number of good genes for the data set to be considered fit for analysis.<br />
If the actual number of good genes falls below this threshold, an error will be<br />
issued.<br />
integer level of verbosity. Zero means silent, higher values make the output<br />
progressively more and more verbose.<br />
indentation for diagnostic messages. Zero means no indentation, each unit adds<br />
two spaces.<br />
Details<br />
The constants ..minNSamples and ..minNGenes are both set to the value 4. For most data sets,<br />
the fraction of missing samples criterion will be much more stringent than the absolute number of<br />
missing samples criterion.
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