Retrieve row index for a set of features

Source: R/celda_functions.R

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
)

Arguments

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.

Value

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

See also

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

Author

Yusuke Koga, Joshua Campbell

Examples

data(celdaCGSim)
retrieveFeatureIndex(c("Gene_1", "Gene_5"), celdaCGSim$counts)
#> [1] 1 5
retrieveFeatureIndex(c("Gene_1", "Gene_5"), celdaCGSim$counts,
                                            exactMatch = FALSE)
#> Warning: Feature 'Gene_1' matched multiple items in 'rownames': Gene_1,Gene_10,Gene_11,Gene_12,Gene_13,Gene_14,Gene_15,Gene_16,Gene_17,Gene_18,Gene_19,Gene_100. Only the first match will be selected.
#> Warning: Feature 'Gene_5' matched multiple items in 'rownames': Gene_5,Gene_50,Gene_51,Gene_52,Gene_53,Gene_54,Gene_55,Gene_56,Gene_57,Gene_58,Gene_59. Only the first match will be selected.
#> [1] 1 5