WGCNA (version 1.34)

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(multiData, rowIndex = NULL, colIndex = NULL, permissive = FALSE, 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

colIndex

A vector giving the columns to be retained. All indexing methods recognized by R can be used (numeric, logical, negative indexing, etc). If NULL, all columns will be retained.

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?

Value

• A multiData structure containing the selected rows and columns. Note that result always retaines it dimension and other attributes.

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.