Convert a list into a SignedIndexList

SignedIndexList(object, ...)

# S4 method for 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 Logical, whether NA indices should be kept or not. Default: FALSE (removed) Logical, whether duplicated indices should be kept or not. Default: FALSE (removed) 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 list of 3 signed indices with offset=1
#> Options: NA removed: TRUE; duplicates removed: TRUE
#>   a[n=5]
#>     positive[n=3]:1,2,4
#>     negative[n=2]:1,3
#>   b (no genes)
#>   c[n=3]
#>     positive[n=3]:2,3,1
#>     negative[n=0]:

## a special case of input is a single list with two elements, \code{pos} and \code{neg}
SignedIndexList(myList[[1]])
#> A list of 1 signed indices with offset=1
#> Options: NA removed: TRUE; duplicates removed: TRUE
#>   NONAME[n=5]
#>     positive[n=3]:1,2,4
#>     negative[n=2]:1,3