GetGeneSets {CAMML}R Documentation

Get Pre-Built Gene Sets to be applied to CAMML


GetGeneSets takes in a one of the following: "immune.cells","skin.immune.cells","T.subset.cells", or "mouse.cells" and a Seurat Object that will be cell-typed using CAMML. The function will then build a gene.set.collection and a list of gene.weights based on one of the pre-built gene sets.


    GetGeneSets(data = "immune.cells")



One of the following: "immune.cells","skin.immune.cells","T.subset.cells", or "mouse.cells".

  • "immune.cells" provides gene sets for 5 human immune cells: B, T, NK, Monocytes, and HSCs.

  • "skin.immune.cells" provides gene sets for 6 human cell types: B, T, NK, Endothelial, Fibroblast, and Monocytes.

  • "T.subset.cells" provides 6 gene sets for 5 human T cell subtypes: naive CD4, CD4, naive CD8, CD8, memory, and regulatory T cells.

  • "mouse.cells" provides gene sets for 7 mouse cell types: B, T, NK, DC, Endothelial, Fibroblasts, and Macrophages.

All datasets were built using differential expression of data in the package celldex using the package EdgeR.


A data.frame with the cell type, gene name, ensembl ID, and weight for each gene in each gene set.

See Also,



[Package CAMML version 0.2.2 Index]