getFeatures: Get features (methods)

In HELP: Tools for HELP data analysis

Description

Fetch a subset of features from a given data structure

Usage

getFeatures(x, y, ...)

Arguments

x	the matrix of feature data to subset. If x is a vector it is interpreted as a matrix. x can also be of class "ExpressionSet" or an "AnnotatedDataFrame" object.
y	which feature(s) to use. Can be a vector of characters matching feature names, integers indicating which features to choose, or a mixture of the two. If not supplied (or if equivalent to "*"), all features will be used.
...	other arguments passed are not handled at this time.

Value

Returns a matrix of values corresponding to a subset of features from the data structure supplied, where columns correspond to features. Function halts if no features to return.

Author(s)

Reid F. Thompson ([e-mail])

See Also

getFeatures-methods

Examples

data(sample.ExpressionSet)
df <- data.frame(x=1:500,y=501:1000, row.names=featureNames(sample.ExpressionSet))
featureData(sample.ExpressionSet) <- new("AnnotatedDataFrame", data=df, dimLabels=c("featureNames", ""))
getFeatures(sample.ExpressionSet, "y")[1:10]

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")'.

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HELP documentation built on Nov. 8, 2020, 11:08 p.m.