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