R: Find cell types associated with a given gene list

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 1.2.0 Index]