SignedIndexList: Convert a list into a SignedIndexList

In Accio/BioQC: Detect tissue heterogeneity in expression profiles with gene sets

Description

Convert a list into a SignedIndexList

Usage

SignedIndexList(object, ...)

## S4 method for signature 'list'
SignedIndexList(object, keepNA = FALSE, keepDup = FALSE, offset = 1L)

Arguments

object	A list of lists, each with two elements named 'pos' or 'neg', can be logical vectors or integer indices
...	additional arguments, currently ignored
keepNA	Logical, whether NA indices should be kept or not. Default: FALSE (removed)
keepDup	Logical, whether duplicated indices should be kept or not. Default: FALSE (removed)
offset	offset; 1 if missing

Value

A SignedIndexList, a list of lists, containing two vectors named 'positive' and 'negative', which contain the indices of genes that are either positively or negatively associated with a certain phenotype

Examples

myList <- list(a = list(pos = list(1, 2, 2, 4), neg = c(TRUE, FALSE, TRUE)), 
b = list(NA), c = list(pos = c(c(2, 3), c(1, 3))))
SignedIndexList(myList)

## a special case of input is a single list with two elements, \code{pos} and \code{neg}
SignedIndexList(myList[[1]])

Accio/BioQC documentation built on Jan. 27, 2022, 10:45 p.m.