IndexList: Convert a list to an IndexList object

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

Description

Convert a list to an IndexList object

Usage

IndexList(object, ..., keepNA = FALSE, keepDup = FALSE, offset = 1L)

## S4 method for signature 'numeric'
IndexList(object, ..., keepNA = FALSE, keepDup = FALSE, offset = 1L)

## S4 method for signature 'logical'
IndexList(object, ..., keepNA = FALSE, keepDup = FALSE, offset = 1L)

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

Arguments

object	Either a list of unique integer indices, NULL and logical vectors (of same lengths), or a numerical vector or a logical vector. NA is discarded.
...	If object isn't a list, additional vectors can go here.
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	Integer, the starting index. Default: 1 (as in the convention of R)

Value

The function returns a list of vectors

Examples

testList <- list(GS_A=c(1,2,3,4,3),
                 GS_B=c(2,3,4,5),
                 GS_C=NULL,
                 GS_D=c(1,3,5,NA),
                 GS_E=c(2,4))
testIndexList <- IndexList(testList)
IndexList(c(FALSE, TRUE, TRUE), c(FALSE, FALSE, TRUE), c(TRUE, FALSE, FALSE), offset=0)
IndexList(list(A=1:3, B=4:5, C=7:9))
IndexList(list(A=1:3, B=4:5, C=7:9), offset=0)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

A list of 3 indices with offset=0
Options: NA removed: TRUE; duplicates removed: TRUE
  NONAME (n=2): 2,3
  NONAME (n=1): 3
  NONAME (n=1): 1
A list of 3 indices with offset=1
Options: NA removed: TRUE; duplicates removed: TRUE
  A (n=3): 1,2,3
  B (n=2): 4,5
  C (n=3): 7,8,9
A list of 3 indices with offset=0
Options: NA removed: TRUE; duplicates removed: TRUE
  A (n=3): 1,2,3
  B (n=2): 4,5
  C (n=3): 7,8,9

BioQC documentation built on Nov. 8, 2020, 7:16 p.m.