WGCNA: imputeByModule – R documentation

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imputeByModule

Impute missing data separately in each module

Use impute.knn to ipmpute missing data, separately in each module.

imputeByModule(
  data, 
  labels, 
  excludeUnassigned = FALSE, 
  unassignedLabel = if (is.numeric(labels)) 0 else "grey", 
  scale = TRUE, 
  ...)

`data`	Data to be imputed, with variables (genes) in columns and observations (samples) in rows.
`labels`	Module labels. A vector with one entry for each column in `data`.
`excludeUnassigned`	Logical: should unassigned variables (genes) be excluded from the imputation?
`unassignedLabel`	The value in `labels` that represents unassigned variables.
`scale`	Logical: should `data` be scaled to mean 0 and variance 1 before imputation?
`...`	Other arguments to `impute.knn`.

The input data with missing values imputed.

This function is potentially faster but could give different imputed values than applying impute.knn directly to (scaled) data.

Peter Langfelder