imputeByModule {WGCNA}

Impute missing data separately in each module

Description

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

Usage

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

Arguments

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.

Value

The input data with missing values imputed.

Note

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

Author(s)

Peter Langfelder

See Also

impute.knn that does the actual imputation.