gene_list_generation: Extracting genes for phenotype/diseases from NCBI.

In nanotatoR: 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, term, outpath, thresh = 5, returnMethod = c("Text",
  "dataFrame"))

Arguments

method_entrez	character. Input Method for terms. Choices are "Single","Multiple" and "Text".
termPath	character. Path and file name for textfile.
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.

Value

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

Examples

terms="Muscle Weakness"
genes <- gene_list_generation(method="Single", term=terms, returnMethod="dataFrame")

nanotatoR documentation built on Nov. 8, 2020, 6:54 p.m.