Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
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46 goodSamplesMS<br />
verbose<br />
indent<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 />
This function iteratively identifies samples and genes with too many missing entries and genes with<br />
zero variance. Iterations may be required since excluding samples effectively changes criteria on<br />
genes and vice versa. The process is repeated until the lists of good samples and genes are stable.<br />
The constants ..minNSamples and ..minNGenes are both set to the value 4.<br />
Value<br />
A list with the foolowing components:<br />
goodSamples<br />
goodGenes<br />
A logical vector with one entry per sample that is TRUE if the sample is considered<br />
good and FALSE otherwise.<br />
A logical vector with one entry per gene that is TRUE if the gene is considered<br />
good and FALSE otherwise.<br />
Author(s)<br />
Peter Langfelder<br />
See Also<br />
goodSamples, goodGenes<br />
goodSamplesMS<br />
Filter samples with too many missing entries across multiple data sets<br />
Description<br />
This function checks data for missing entries and returns a list of samples that pass two criteria on<br />
maximum number of missing values: the fraction of missing values must be below a given threshold<br />
and the total number of missing genes must be below a given threshold.<br />
Usage<br />
goodSamplesMS(multiExpr,<br />
useSamples = NULL,<br />
useGenes = NULL,<br />
minFraction = 1/2,<br />
minNSamples = ..minNSamples,<br />
minNGenes = ..minNGenes,<br />
verbose = 1, indent = 0)
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