channelNames: Retrieve and set channel names from object

In Biobase: Biobase: Base functions for Bioconductor

Description

This generic function reports or updates the channels in an object.

Usage

channelNames(object, ...)
channelNames(object, ...) <- value

Arguments

object	An S4 object, typically derived from class eSet
value	Replacement value, either a character vector (to re-order existing channel names or a named character vector or list (to change channel names from the vector elements to the corresponding names).
...	Additional argument, not currently used.

Details

channelNames returns the names of the channels in a defined order. Change the order using the replacement method with a permuation of the channel names as value. Rename channels using the replacement method with a named list, where the vector elements are a permutation of the current channels, with corresponding names the new identifier for the channel.

Value

character.

Author(s)

Biocore

Examples

## channelNames default to alphabetical order of channels
obj <- NChannelSet(
           R=matrix(runif(100), 20, 5),
           G=matrix(-runif(100), 20, 5))
channelNames(obj)
channelNames(obj) <- c(Gn="G", Rd="R")   ## rename
channelNames(obj)
channelNames(obj) <- c("Rd", "Gn")       ## reorder
channelNames(obj)
all(assayData(obj)[["Gn"]] <= 0)
all(assayData(obj)[["Rd"]] >= 0)

Example output

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':

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

[1] "G" "R"
[1] "Gn" "Rd"
[1] "Rd" "Gn"
[1] TRUE
[1] TRUE

Biobase documentation built on Nov. 8, 2020, 6:52 p.m.