NCBI_synonyms: Automatic NCBI annotation for human gene lists

In wizbionet/wizbionet: non-coding RNAs data integrator and prioritizer

Description

This function uses NCBI nomenclature which allows merging diffrent human gene lists using identical gene names. It also provides Entrez genes IDs and ENSEMBL gene IDs. It utilizez pre-processed annotation file downloaded from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz .

Usage

NCBI_synonyms(inputDF, input_col)

Arguments

inputDF	data frame with column containing gene symbols
input_col	name of the column containing gene symbols

Value

output is a original data frame with additional columns "SymbolNCBI" ,"EntrezID" , "ENSG_ID"

Author(s)

Zofia Wicik

References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

Examples

inputDF<- data.frame(
symbols=c('ONECUT2','NEBL','SNTB2','USP9Y','KAT6A','CRIM1','IGSF10'),
values=c(0.01,0.5,0.05,0.001,0.9,0.03,0.06))
input_col<- "symbols"
output<-wizbionet::NCBI_synonyms(inputDF, input_col)
names(output)

wizbionet/wizbionet documentation built on Sept. 9, 2020, 12:45 a.m.