subsetSCERows {singleCellTK} | R Documentation

## Subset a SingleCellExperiment object by rows

### Description

Used to peform subsetting of a SingleCellExperiment object using a variety of methods that indicate the correct rows to keep. The various methods, `index`, `bool`, and `rowData`, can be used in conjunction with one another. If `returnAsAltExp` is set to `TRUE`, then the returned object will have the same number of rows as the input `inSCE` as the subsetted object will be stored in the `altExp` slot.

### Usage

    subsetSCERows(
      inSCE,
      index = NULL,
      bool = NULL,
      rowData = NULL,
      returnAsAltExp = TRUE,
      altExpName = "subset",
      prependAltExpName = TRUE
    )

### Arguments

`inSCE` | Input SingleCellExperiment object.
`index` | Integer vector. Vector of indicies indicating which rows to keep. If `NULL`, this will not be used for subsetting. Default `NULL`.
`bool` | Boolean vector. Vector of `TRUE` or `FALSE` indicating which rows should be kept. Needs to be the same length as the number of rows in `inSCE`. If `NULL`, this will not be used for subsetting. Default `NULL`.
`rowData` | Character. An expression that will identify a subset of rows using variables found in the `rowData` of `inSCE`. For example, if `x` is a numeric vector in `rowData`, then `"x < 5"` will return all rows with x less than 5. Single quotes should be used for character strings. For example, `"y == 'yes'"` will return all rows where y is "yes". Multiple expressions can be evaluated by placing them in a vector. For example `c("x < 5", "y =='yes'")` will apply both operations for subsetting. If `NULL`, this will not be used for subsetting. Default `NULL`.
`returnAsAltExp` | Boolean. If `TRUE`, the subsetted SingleCellExperiment object will be returned in the `altExp` slot of `inSCE`. If `FALSE`, the subsetted SingleCellExperiment object will be directly returned.
`altExpName` | Character. Name of the alternative experiment object to add if `returnAsAltExp = TRUE`. Default `subset`.
`prependAltExpName` | Boolean. If `TRUE`, `altExpName` will be added to the beginning of the assay names in the `altExp` object. This is only utilized if `returnAsAltExp = TRUE`. Default `TRUE`.

### Value

A SingleCellExperiment object that has been subsetted by rowData.

### Author(s)

Joshua D. Campbell

### Examples

    data(scExample)

    # Set a variable up in the rowData indicating mitochondrial genes
    rowData(sce)$isMito <- ifelse(grepl("^MT-", rowData(sce)$feature_name),
                                  "yes", "no")
    sce <- subsetSCERows(sce, rowData = "isMito == 'yes'")

[Package singleCellTK version 2.2.0 Index]