featureIndex: Retrieve row index for a set of features
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Value Author(s) See Also Examples

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
)

`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`.

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

Yusuke Koga, Joshua D. Campbell

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

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