inferSpecies: Infer species from list of Ensemble ids

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Infer species from list of Ensemble ids

Description

For given gene expression matrix, assign species to each cell (column) based on Ensemble IDs.

Usage

inferSpecies(exp.mat, expected.species, rep.ens.method = "orig")

Arguments

exp.mat	Expression matrix (genes x cell); row names are ensemble IDs, col names are cell IDs.
expected.species	Character vector specifying which species are expected in expression matrix. "Mm" - Mouse "Hs" - Human c("Mm", "Hs") - Mouse and Human.
rep.ens.method	Method used to sample representative Ensemble ID for each cell (i.e., column). "orig" - Original method; computation slower than alternative. "alt" - Default. Alternative method;

Value

Character vector specifying species of each cell in expression matrix.

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.