get_GO_exp: Preprocess Gene Expression
In tinglab/redPATH: Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.

This function reduces the gene expression matrix to selected Gene Ontology genes.

1 2	get_GO_exp(gene_cell_matrix, gene_type = "gene_names", organism = "mouse", takelog = T)

`gene_cell_matrix`	A genes (row) by cells (col) matrix.
`gene_type`	The type of gene names. Default is "gene_names" - ie "HOPX", alternatively "entrez" is provided.
`organism`	The type of species the dataset belongs to: defaults to "mouse". "human" option is available.
`takelog`	Defaults to TRUE. Whether to perform log2(exprs + 1)

1 2	subset_GO_data <- get_GO_exp(data, gene_type = "gene_names", organism = "human", takelog = F) filtered_GO_data <- filter_exp(subset_GO_data, dispersion_threshold = 10, threads = 2)

tinglab/redPATH documentation built on May 31, 2019, 10:37 a.m.

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