retrieveSCEIndex {singleCellTK} | R Documentation

## Retrieve cell/feature index by giving identifiers saved in col/rowData

### Description

Originally written in `retrieveFeatureIndex`. Modified for also retrieving cell indices and only working for SingleCellExperiment object. This will return indices of features among the `rowData`/`colData`. Partial matching (i.e. grepping) can be used.

### Usage

    retrieveSCEIndex(
      inSCE,
      IDs,
      axis,
      by = NULL,
      exactMatch = TRUE,
      firstMatch = TRUE
    )

### Arguments

`inSCE` | Input SingleCellExperiment object. Required
`IDs` | Character vector of identifiers for features or cells to find in `rowData` or `colData` of `inSCE`
`axis` | A character scalar to specify whether to search for features or cells. Use `"row"`, `"feature"` or `"gene"` for features; `"col"` or `"cell"` for cells.
`by` | Character. In which column to search for features/cells in `rowData`/`colData`. Default `NULL` for search the `rownames`/`colnames`
`exactMatch` | A logical scalar. Whether to only identify exact matches or to identify partial matches using `grep`. Default `TRUE`
`firstMatch` | A logical scalar. Whether to only identify the first matches or to return all plausible matches. Default `TRUE`

### Value

A unique, non-NA numeric vector of indices for the matching features/cells in `inSCE`.

### Author(s)

Yusuke Koga, Joshua Campbell

### Examples

    data(scExample, package = "singleCellTK")
    retrieveSCEIndex(inSCE = sce, IDs = "ENSG00000205542",
     axis = "row")

[Package singleCellTK version 2.2.0 Index]