convertGeneIds: Change Gene Identifiers

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Change Gene Identifiers

Description

Changes gene identifiers by aggregating expression measures (sum). This is mainly useful when changing from Ensembl IDs to Gene Symbols

Usage

convertGeneIds(exp, newIds)

Arguments

exp	expression matrix (genes x cells)
newIds	character vector specifying the new identifer that corresponds with each row of the input exp matrix

Details

This method is made fast by the use of sparse matrix multiplication

i.e.: (newIds x oldIds) x (oldIds x cells) = (newIds x cells)

Value

a matrix in which rows with duplicate 'newIds' have been summed together

Examples

exp <- matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3), nrow=3)
colnames(exp) <- c("Cell1", "Cell2", "Cell3")
print(exp)

newIds <- c("GeneA", "GeneA", "GeneB")

result <- convertGeneIds(exp, newIds)
print(result)

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.