Update gene modules — update_gene

Change the gene modules of an MCView app.

Usage

update_gene_modules(project, dataset, gene_modules_file)

Arguments

project: path to the project
dataset: name for the dataset, e.g. "PBMC". The name of the dataset can only contain alphanumeric characters, dots, dashes and underscores.
gene_modules_file: path to a tabular file (csv,tsv) with assignment of genes to gene modules. Should have a field named "gene" with the gene name and a field named "module" with the name of the gene module.

Details

This is usually done after a first iteration of annotation using the "Gene modules" tab in the MCView annotation, which can export a valid gene_modules_file. The file should have a column named "gene" with the gene names and another column named "module" with the id of the gene module. Note that the exported file from the __MCView__ app might contain additional fields which will be ignored in this function.

Under the hood - MCView updates a file named "gene_modules.tsv" under project/cache/dataset, which can also be edited manually.

Examples

if (FALSE) { # \dontrun{
update_gene_modules("PBMC", "PBMC163k", "raw/gene-modules.csv")
} # }