GetGeneSets {CAMML}

Get Pre-Built Gene Sets to be applied to CAMML

Description

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.

Usage

    GetGeneSets(data = "immune.cells")

Arguments

data

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.

Value

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

See Also

org.Hs.eg.db,org.Mm.eg.db

Examples

GetGeneSets("immune.cells")