get_organism_indices {DamageDetective}R Documentation

Retrieve genes corresponding to the organism of interest

Description

Retrieve genes corresponding to the organism of interest

Usage

get_organism_indices(count_matrix, organism)

Arguments

count_matrix

Matrix or dgCMatrix containing the counts from single cell RNA sequencing data.

organism

String specifying the organism of origin of the input data where there are two standard options,

  • "Hsap"

  • "Mmus"

If a user wishes to use a non-standard organism they must input a list containing strings for the patterns to match mitochondrial and ribosomal genes of the organism. If available, nuclear-encoded genes that are likely retained in the nucleus, such as in nuclear speckles, must also be specified. An example for humans is below,

  • organism = c(mito_pattern = "^MT-", ribo_pattern = "^(RPS|RPL)", nuclear <- c("NEAT1","XIST", "MALAT1")

  • Default is "Hsap"

Value

List containing the indices of the count matrix corresponding to mitochondrial, non-mitochondrial, and ribosomal gene sets.


[Package DamageDetective version 1.0.0 Index]