retrieveFeatureIndex: Retrieve row index for a set of features
In celda: CEllular Latent Dirichlet Allocation

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.

retrieveFeatureIndex(
  features,
  x,
  by = "rownames",
  exactMatch = TRUE,
  removeNA = FALSE
)

`features`	Character vector of feature names to find in the rows of `x`.
`x`	A data.frame, matrix, or SingleCellExperiment object to search.
`by`	Character. Where to search for features in `x`. If set to `"rownames"` then the features will be searched for among `rownames(x)`. If `x` inherits from class SummarizedExperiment, then `by` can be one of the fields in the row annotation data.frame (i.e. one of `colnames(rowData(x))`).
`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 `x` 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`.

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

Yusuke Koga, Joshua Campbell

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

data(celdaCGSim)
retrieveFeatureIndex(c("Gene_1", "Gene_5"), celdaCGSim$counts)
retrieveFeatureIndex(c("Gene_1", "Gene_5"), celdaCGSim$counts,
                                            exactMatch = FALSE)