subEset: Subset an ExpressionSet to values of phenotypic data columns.

In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description

Given a list of column names and corresponding values present in the phenoData slot of an ExpressionSet object, this method returns the subset of the ExpressionSet restricted to samples associated with the given values in the given columns.

Usage

    subEset(eSet, subset = list())

Arguments

eSet

ExpressionSet of the Biobase package including a gene-by-sample expression matrix in the AssayData slot, and a phenotypic information data-frame in the phenodate slot. In the expression matrix, row names are Ensembl gene identifiers or probeset identifiers, and column names are sample identifiers. In the phentypic data-frame, row names are sample idenfifiers, column names are grouping factors and phenotypic traits usable for the one-way ANOVA.

subset

A named list to subset eSet. Names must be column names existing in colnames(pData(eSet)). Values must be vectors of values existing in the corresponding column of pData(eSet).

Value

A subset of the given ExpressionSet restricted to samples associated with the given values in the given columns

Author(s)

Kevin Rue-Albrecht

See Also

Class ExpressionSet.

Examples

# Load example data set
data(AlvMac)

# Subset it to only samples of "CN" and "MB" treatments, and also only "2H",
# "6H", and "24H" time-points
sub.AlvMac <- subEset(
    eSet=AlvMac,
    subset=list(
        Treatment=c("CN","MB"),
        Time=c("2H","6H")
        )
    )

Example output

Loading required package: grid
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, cbind, colMeans, colSums, colnames, 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

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GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.