subsetSCERows: Subset a SingleCellExperiment object by rows
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Value Author(s) Examples

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.

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

`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`.

A SingleCellExperiment object that has been subsetted by rowData.

Joshua D. Campbell

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'")