gene_list_generation {nanotatoR} | R Documentation |
Extracting genes for phenotype/diseases from NCBI.
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 )
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. |
Text files containg gene list and terms associated with them are stored as text files.
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)