R: Obtain the gene module of a gene of interest

featureModuleLookup {celda}

R Documentation

Obtain the gene module of a gene of interest

Description

This function will output the corresponding feature module for a specified vector of genes from a celda_CG or celda_G celdaModel. feature must match the rownames of sce.

Usage

featureModuleLookup(sce, ...)

## S4 method for signature 'SingleCellExperiment'
featureModuleLookup(
  sce,
  feature,
  altExpName = "featureSubset",
  exactMatch = TRUE
)

Arguments

`sce`	A SingleCellExperiment object returned by celda_G, or celda_CG, with the matrix located in the `useAssay` assay slot. Rows represent features and columns represent cells.
`...`	Ignored. Placeholder to prevent check warning.
`feature`	Character vector. Identify feature modules for the specified feature names. `feature` must match the rownames of `sce`.
`altExpName`	The name for the altExp slot to use. Default "featureSubset".
`exactMatch`	Logical. Whether to look for exactMatch of the gene name within counts matrix. Default `TRUE`.

Value

List. Each entry corresponds to the feature module determined for the provided features.

Examples

data(sceCeldaCG)
module <- featureModuleLookup(sce = sceCeldaCG,
    feature = c("Gene_1", "Gene_XXX"))

[Package celda version 1.6.1 Index]