Mito_umi_gn: Mito_umi_gn function

In alimahdipour/sciCNV: sciCNV

Mito_umi_gn function

Description

Function to sketch mitochondrial transcript content, nUMI and nGene data at cellular level to detect damaged cells within the population

Usage

Mito_umi_gn(mat, percent.mito.G, nUMI, nGene, No.test, drop.mads = 3)

Arguments

mat	raw data matrix
percent.mito.G	percentage of mitochondrial transcripts relative to total number of reads per cell
nUMI	number of unified molecular identification (UMI)
nGene	number of expressed genes
No.test	number of test cells included in the data; can be used to delineate the populations of test and control cells in the heatmap
drop.mads	number of the median absolute deviation (MAD) to drop damaged cells using the percentage of mitochondrial expression level

Value

The output represents damaged cells due to the given for mitochondrial percentage cutoff

Note

Please refer to the reference and supplemental materials described in the README for additional details.

Author(s)

Ali Mahdipour-Shirayeh, Princess Margaret Cancer Centre, University of Toronto

Examples

damaged_cells <- Mito_umi_gn(mat=raw_data, percent.mito.G, nUMI, nGene, No.test=100, drop.mads = 3)

alimahdipour/sciCNV documentation built on Oct. 16, 2022, 12:56 p.m.