commonIds: Get the name of the ids common to all datasets

In MultiDataSet: Implementation of MultiDataSet and ResultSet

Description

Get the name of the ids common to all datasets

Usage

commonIds(object)

Arguments

object

MultiDataSet that will be filtered.

Value

Character vector with the common ids.

Examples

 
multi <- createMultiDataSet()
eset <- new("ExpressionSet", exprs = matrix(runif(9), ncol = 3))
fData(eset) <- data.frame(chromosome = c("chr1", "chr1", "chr1"), 
                          start = c(1, 5, 10),end = c(4, 6, 14), 
                          stringsAsFactors = FALSE)
sampleNames(eset) <- c("S1", "S2", "S3")
pData(eset) <- data.frame(id = c("S1", "S2", "S3"))
rownames(pData(eset)) <- c("S1", "S2", "S3")
multi <- add_genexp(multi, eset, dataset.name = "g1")
eset <- new("ExpressionSet", exprs = matrix(runif(8), ncol = 2))
fData(eset) <- data.frame(chromosome = c("chr1", "chr1", "chr1", "chr1"), 
                          start = c(1, 14, 25, 104),end = c(11, 16, 28, 115),
                          stringsAsFactors = FALSE)
sampleNames(eset) <- c("S1", "G2")
pData(eset) <- data.frame(id = c("S1", "G2"))
rownames(pData(eset)) <- c("S1", "G2")

multi <- add_genexp(multi, eset, dataset.name="g2")
commonIds(multi)

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':

    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")'.

Warning messages:
1: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
2: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind' 
[1] "S1"

MultiDataSet documentation built on Jan. 31, 2021, 2:01 a.m.