featureModuleLookup: Obtain the gene module of a gene of interest

In celda: CEllular Latent Dirichlet Allocation

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"))

celda documentation built on Nov. 8, 2020, 8:24 p.m.