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)

Value

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

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?

Author

Peter Langfelder

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).