write_scite_inputs: Write input files for SCITE

In northNomad/tapestri.tools: A toolbox for the analysis of tapestri single cell multi-omics data

Write input files for SCITE

Description

A helper function to write genotype matrix and .geneNames files for SCITE.

Usage

write_scite_inputs(h5f, variants, cell_index = NULL, fp_ngt_csv, fp_geneNames)

Arguments

h5f	h5f
variants	A named vector. You should get the value from the id column after calling get_variants. The names should be meaningful, they are the labels in your inferred clonal architecture .gv file. Avoid symbols like ., -, : in the names, and use an underscore _ instead.
cell_index	A numeric vector. Specifies which cells (columns) to retrieve.
fp_ngt_csv	Output file name for NGT matrix .csv
fp_geneNames	Output file name for .geneNames

Value

NULL. Writes two files.

References

https://github.com/cbg-ethz/SCITE

Kuipers J et al. Single-cell sequencing data reveals widespread recurrence and loss of mutational hits in the life histories of tumorus. Genome Research 2017; 27:1885-1894.

northNomad/tapestri.tools documentation built on May 31, 2024, 4:44 p.m.