remove_duplicate_genes: Remove duplicate gene symbol on a gene expression data

In IOBR/IOBR: Immune Oncology Biological Research

Remove duplicate gene symbol on a gene expression data

Description

Remove duplicate gene symbol on a gene expression data

Usage

remove_duplicate_genes(eset, column_of_symbol, method = "mean")

Arguments

eset	Gene expression data with gene symbol in 'column_of_symbol'
column_of_symbol	name of column contained gene symbols
method	method used to filter duplicate genes; default is mean value

Author(s)

Dongqiang Zeng

Examples

# loading eset
data("eset_stad", package = "IOBR")
# annotation
eset_stad <- anno_eset(eset = eset_stad, annotation = anno_rnaseq)
eset_stad <- rownames_to_column(eset_stad, var = "id")

# Creating duplicate gene names
eset_stad[2:3, "id"] <- "MT-CO1"
# Counting the number of identical names
summary(duplicated(eset_stad$id))
# De-duplication of rows with the same gene name using the average value
eset_stad<-remove_duplicate_genes(eset = eset_stad, column_of_symbol = "id", method = "mean")
summary(duplicated(eset_stad$id))

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.