findCellType {scfind} | R Documentation

## Find cell types associated with a given gene list

### Description

Calculates p-values of a log-likelihood of a list of genes to be associated with each cell type. Log-likelihood is based on gene expression values.

### Usage

    findCellType(gene_index = NULL, gene_list = NULL)

    findCellType.data.frame(gene_index, gene_list)

    ## S4 method for signature 'data.frame'
    findCellType(gene_index = NULL, gene_list = NULL)

### Arguments

`gene_index` | a data.frame with cell types in columns and genes in rows
`gene_list` | genes that need to be searched in the gene_index

### Value

a named numeric vector containing p-values

### Examples

    library(SingleCellExperiment)
    sce <- SingleCellExperiment(assays = list(normcounts = as.matrix(yan)), colData = ann)
    # this is needed to calculate dropout rate for feature selection
    # important: normcounts have the same zeros as raw counts (fpkm)
    counts(sce) <- normcounts(sce)
    logcounts(sce) <- log2(normcounts(sce) + 1)
    # use gene names as feature symbols
    rowData(sce)$feature_symbol <- rownames(sce)
    isSpike(sce, 'ERCC') <- grepl('^ERCC-', rownames(sce))
    # remove features with duplicated names
    sce <- sce[!duplicated(rownames(sce)), ]
    index <- buildCellTypeIndex(sce)
    res <- findCellType(index, gene_list = c('SOX6', 'SNAI3'))

[Package scfind version 1.4.1 Index]