gene_info: Gene information

In jmonlong/scCNAutils: Functions to analyze copy number aberrations in single-cell data

Gene information

Description

Computes information at the gene level that can be used to annotate the results later (e.g. CNA calls).

Usage

gene_info(ge_df, genes_coord, subset_cells = 10000)

Arguments

ge_df	a data.frame with gene expression information across cells. E.g. after norm.ge.
genes_coord	either a file name or a data.frame with coordinates and gene names.
subset_cells	the maximum number of cells to use.

Details

If the input data.frame has a symbol column, 'genes_coord' is used to add the coordinates, later used to overlap with region/CNA calls. If the input data.frame has coordinates, 'genes_coord' is used to retrieve the gene name. In both cases a row in the input data.frame must be a gene, not a bin.

It's better to run this function after normalization (norm_ge but before binning (bin_genes).

Value

a data.frame with summary stats for each gene.

Author(s)

Jean Monlong

jmonlong/scCNAutils documentation built on Feb. 8, 2025, 8:09 a.m.