rev_gene: Pre-processing step: revising gene symbols

In scCATCH: Single Cell Cluster-Based Annotation Toolkit for Cellular Heterogeneity

Pre-processing step: revising gene symbols

Description

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

Usage

rev_gene(data = NULL, data_type = NULL, species = NULL, geneinfo = NULL)

Arguments

data	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 demo_marker.
data_type	A character to define the type of data, select 'data' for the data matrix, 'marker' for the data.frame containing cell markers.
species	Species of the data.'Human' or 'Mouse'.
geneinfo	A data.frame of the system data containing gene symbols of 'Human' and 'Mouse' updated on Jan. 1, 2022.

Value

A new matrix or data.frame.

scCATCH documentation built on April 23, 2023, 5:09 p.m.