rev_gene

Revise genes according to NCBI Gene symbols updated in June 19, 2022 for count matrix, user-custom cell marker data.frame.

An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) <doi:10.1016/j.isci.2020.100882> for more details.

Xin Shao

scCATCH

Single Cell Cluster-Based Annotation Toolkit for Cellular
Heterogeneity

rev_gene function

<dl><dt>data</dt>
<dd>A matrix or dgCMatrix containing count or normalized data, each column representing a spot or a cell, each row representing a gene; Or a data.frame containing cell markers, use <code>demo_marker</code>.</dd>
<dt>data_type</dt>
<dd>A character to define the type of <code>data</code>, select <code>'data'</code> for the data matrix, <code>'marker'</code> for the data.frame containing cell markers.</dd>
<dt>species</dt>
<dd>Species of the data.<code>'Human'</code> or <code>'Mouse'</code>.</dd>
<dt>geneinfo</dt>
<dd>A data.frame of the system data containing gene symbols of <code>'Human'</code> and <code>'Mouse'</code> updated on Jan. 1, 2022.</dd></dl>

Arguments

Pre-processing step: revising gene symbols — rev_gene

<dl>

<dt>data</dt>
<dd>A matrix or dgCMatrix containing count or normalized data, each column representing a spot or a cell, each row representing a gene; Or a data.frame containing cell markers, use <code>demo_marker</code>.</dd>


<dt>data_type</dt>
<dd>A character to define the type of <code>data</code>, select <code>'data'</code> for the data matrix, <code>'marker'</code> for the data.frame containing cell markers.</dd>


<dt>species</dt>
<dd>Species of the data.<code>'Human'</code> or <code>'Mouse'</code>.</dd>


<dt>geneinfo</dt>
<dd>A data.frame of the system data containing gene symbols of <code>'Human'</code> and <code>'Mouse'</code> updated on Jan. 1, 2022.</dd>

</dl>

rev_gene: Pre-processing step: revising gene symbols

Description

Usage

Value

Arguments