WGCNA: mtd.subset – R documentation

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WGCNA

mtd.subset

Subset rows and columns in a multiData structure

Description

The function restricts each data component to the given columns and rows.

Usage

mtd.subset(
  # Input
  multiData, 

  # Rows and columns to keep
  rowIndex = NULL, colIndex = NULL, 
  invert = FALSE,

  # Strict or permissive checking of structure?
  permissive = FALSE, 

  # Output formatting options
  drop = FALSE)

Arguments

`multiData`	A multiData structure.
`rowIndex`	A list in which each component corresponds to a set and is a vector giving the rows to be retained in that set. All indexing methods recognized by R can be used (numeric, logical, negative indexing, etc). If `NULL`, all columns will be retained in each set. Note that setting individual elements of `rowIndex` to `NULL` will lead to errors.
`colIndex`	A vector giving the columns to be retained. All indexing methods recognized by R can be used (numeric, logical, negative indexing, etc). In addition, column names of the retained columns may be given; if a given name cannot be matched to a column, an error will be thrown. If `NULL`, all columns will be retained.
`invert`	Logical: should the selection be inverted?
`permissive`	Logical: should the function tolerate "loose" `multiData` input? Note that the subsetting may lead to cryptic errors if the input `multiData` does not follow the "strict" format.
`drop`	Logical: should dimensions with extent 1 be dropped?

Details

A multiData structure is intended to store (the same type of) data for multiple, possibly independent, realizations (for example, expression data for several independent experiments). It is a list where each component corresponds to an (independent) data set. Each component is in turn a list that can hold various types of information but must have a data component. In a "strict" multiData structure, the data components are required to each be a matrix or a data frame and have the same number of columns. In a "loose" multiData structure, the data components can be anything (but for most purposes should be of comparable type and content).

This function assumes a "strict" multiData structure unless permissive is TRUE.

Value

A multiData structure containing the selected rows and columns. Attributes (except possibly dimensions and the corresponding dimnames) are retained.

Author(s)

Peter Langfelder