Joshua D. Campbell authored on 28/06/2020 19:18:31
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/featureIndex.R |
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+\name{featureIndex}
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+\alias{featureIndex}
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+\title{Retrieve row index for a set of features}
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+\usage{
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+featureIndex( |
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+ features, |
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+ inSCE, |
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+ by = "rownames", |
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+ exactMatch = TRUE, |
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+ removeNA = FALSE, |
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+ errorOnNoMatch = TRUE, |
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+ warningOnPartialMatch = TRUE |
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+) |
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+} |
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+\arguments{
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+\item{features}{Character vector of feature names to find in the rows of
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+\code{inSCE}.}
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+ |
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+\item{inSCE}{A data.frame, matrix, or \linkS4class{SingleCellExperiment}
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+object to search.} |
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+ |
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+\item{by}{Character. Where to search for features in \code{inSCE}. If set to
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+\code{"rownames"} then the features will be searched for among
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+\code{rownames(inSCE)}. If \code{inSCE} inherits from class
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+\linkS4class{SummarizedExperiment}, then \code{by} can be one of the
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+fields in the row annotation data.frame (i.e. one of |
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+\code{colnames(rowData(inSCE))}).}
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+ |
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+\item{exactMatch}{Boolean. Whether to only identify exact matches
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+or to identify partial matches using \code{\link{grep}}.}
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+ |
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+\item{removeNA}{Boolean. If set to \code{FALSE}, features not found in
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+\code{inSCE} will be given \code{NA} and the returned vector will be the same
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+length as \code{features}. If set to \code{TRUE}, then the \code{NA}
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+values will be removed from the returned vector. Default \code{FALSE}.}
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+ |
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+\item{errorOnNoMatch}{Boolean. If \code{TRUE}, an error will be given if
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+no matches are found. If \code{FALSE}, an empty vector will be returned if
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+\code{removeNA} is set to \code{TRUE} or a vector of \code{NA} if
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+\code{removeNA} is set to \code{FALSE}. Default \code{TRUE}.}
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+ |
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+\item{warningOnPartialMatch}{Boolean. If \code{TRUE}, a warning will be
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+given if some of the entries in \code{features} were not found in
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+\code{inSCE}. The warning will list the features not found.
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+Default \code{TRUE}.}
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+} |
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+\value{
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+A vector of row indices for the matching features in \code{inSCE}.
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+} |
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+\description{
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+This will return indices of features among the rownames |
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+or rowData of a data.frame, matrix, or a \linkS4class{SummarizedExperiment}
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+object including a \linkS4class{SingleCellExperiment}.
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+Partial matching (i.e. grepping) can be used by setting |
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+\code{exactMatch = FALSE}.
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+} |
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+\examples{
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+data(scExample) |
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+ix <- featureIndex(features = c("MT-CYB", "MT-ND2"),
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+ inSCE = sce, |
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+ by = "feature_name") |
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+} |
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+\seealso{
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+'\link[scater]{retrieveFeatureInfo}' from package \code{'scater'}
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+and \code{link{regex}} for how to use regular expressions when
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+\code{exactMatch = FALSE}.
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+} |
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+\author{
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+Yusuke Koga, Joshua D. Campbell |
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+} |