get_organism_indices

Retrieve genes corresponding to the organism of interest

internal

Detects and filters damaged cells in single-cell RNA sequencing
(scRNA-seq) data using a novel approach inspired by 'DoubletFinder'. Damage
is detected by measuring the extent to which cells deviate from
artificially damaged profiles of themselves, simulated through the
probabilistic escape of cytoplasmic RNA. As output, a damage score
ranging from 0 to 1 is given for each cell providing an intuitive scale for
filtering that is standardised across cell types, samples, and experiments.

Alicen Henning

DamageDetective

Detecting Damaged Cells in Single-Cell RNA Sequencing Data

get_organism_indices function

<dl><dt>count_matrix</dt>
<dd>Matrix or dgCMatrix containing the counts from
single cell RNA sequencing data.</dd>
<dt>organism</dt>
<dd>String specifying the organism of origin of the input
data where there are two standard options,<ul>
<li>"Hsap"</li>
<li>"Mmus"</li>
</ul></dd>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,<ul>
<li>organism = c(mito_pattern = "^MT-",
ribo_pattern = "^(RPS|RPL)",
nuclear &lt;- c("NEAT1","XIST", "MALAT1")</li>
<li>Default is "Hsap"</li>
</ul></dl>

Arguments

Retrieve genes corresponding to the organism of interest — get_organism_indices

<dl>

<dt>count_matrix</dt>
<dd>Matrix or dgCMatrix containing the counts from
single cell RNA sequencing data.</dd>


<dt>organism</dt>
<dd>String specifying the organism of origin of the input
data where there are two standard options,<ul>
<li>"Hsap"</li>
<li>"Mmus"</li>
</ul>

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,<ul>
<li>organism = c(mito_pattern = "^MT-",
ribo_pattern = "^(RPS|RPL)",
nuclear &lt;- c("NEAT1","XIST", "MALAT1")</li>
<li>Default is "Hsap"</li>
</ul></dd>

</dl>

get_organism_indices: Retrieve genes corresponding to the organism of interest

Description

Usage

Value

Arguments