gene_list_generation: Extracting genes for phenotype/diseases from NCBI.

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Description

Extracting genes for phenotype/diseases from NCBI.

Usage

gene_list_generation(
  method_entrez = c("Single", "Multiple", "Text"),
  termPath,
  omimID = NULL,
  term,
  outpath,
  thresh = 5,
  returnMethod = c("Text", "dataFrame"),
  omim,
  clinvar,
  gtr,
  removeClinvar = FALSE,
  removeGTR = FALSE,
  downloadClinvar = FALSE,
  downloadGTR = FALSE,
  url_gtr
)

Arguments

method_entrez	character. Input Method for terms. Choices are "Single","Multiple" and "Text".
termPath	character. Path and file name for textfile. FileName should be in the following format "SampleID_Keywords.csv".
omimID	numeric. mimID for disease. Default is NULL.
term	character. Single or Multiple Terms.
outpath	character. Path where gene lists are saved.
thresh	integer. Threshold for the number of terms sent to entrez. Note if large lists are sent to ncbi, it might fail to get processed. Default is 5.
returnMethod	Method of returning output. Options, Text or data.frame.
omim	character. omim2gene file name and location.
clinvar	character. clinvar file name and location.
gtr	character. gtr file name and location.
removeClinvar	logical. Deletes the Clinvar database if TRUE.
removeGTR	logical. Deletes the GTR database if TRUE.
downloadClinvar	logical. Downloads the Clinvar database if TRUE.
downloadGTR	logical. Downloads the GTR database if TRUE.
url_gtr	character. url for GTR.

Value

Text files containg gene list and terms associated with them are stored as text files.

Examples

terms="CIRRHOSIS, FAMILIAL"
genes <- gene_list_generation(
     method_entrez = c("Single"), 
     term = terms,
     returnMethod=c("dataFrame"), 
     omimID = "OMIM:118980",
     omim = system.file("extdata", "mim2gene.txt", package="nanotatoR"), 
     clinvar = system.file("extdata", "localPDB/", package="nanotatoR"), 
     gtr = system.file("extdata", "gtrDatabase.txt", package="nanotatoR"),
     downloadClinvar = FALSE, downloadGTR = FALSE)

VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.