Retrieve row index for a set of features

This will return indices of features among the rownames or rowData of a data.frame, matrix, or a SummarizedExperiment object including a SingleCellExperiment. Partial matching (i.e. grepping) can be used by setting exactMatch = FALSE.

featureIndex(
  features,
  inSCE,
  by = "rownames",
  exactMatch = TRUE,
  removeNA = FALSE,
  errorOnNoMatch = TRUE,
  warningOnPartialMatch = TRUE
)

Arguments

features

Character vector of feature names to find in the rows of inSCE.

inSCE

A data.frame, matrix, or SingleCellExperiment object to search.

by

Character. Where to search for features in inSCE. If set to "rownames" then the features will be searched for among rownames(inSCE). If inSCE inherits from class SummarizedExperiment, then by can be one of the fields in the row annotation data.frame (i.e. one of colnames(rowData(inSCE))).

exactMatch

Boolean. Whether to only identify exact matches or to identify partial matches using grep.

removeNA

Boolean. If set to FALSE, features not found in inSCE will be given NA and the returned vector will be the same length as features. If set to TRUE, then the NA values will be removed from the returned vector. Default FALSE.

errorOnNoMatch

Boolean. If TRUE, an error will be given if no matches are found. If FALSE, an empty vector will be returned if removeNA is set to TRUE or a vector of NA if removeNA is set to FALSE. Default TRUE.

warningOnPartialMatch

Boolean. If TRUE, a warning will be given if some of the entries in features were not found in inSCE. The warning will list the features not found. Default TRUE.

Value

A vector of row indices for the matching features in inSCE.

See also

'retrieveFeatureInfo' from package 'scater' and link{regex} for how to use regular expressions when exactMatch = FALSE.

Author

Yusuke Koga, Joshua D. Campbell

Examples

data(scExample)
ix <- featureIndex(features = c("MT-CYB", "MT-ND2"),
                             inSCE = sce,
                             by = "feature_name")