getClinVarData: getClinVarData

In BIMSBbioinfo/slimR: Short Linear Motif (SLiM) Analysis in the context of human diseases

Description

This function will fetch the clinvar data from the given url and parse the contents of the downloaded file.

Usage

getClinVarData(url = paste0("ftp://ftp.ncbi.nlm.nih.gov/",
  "pub/clinvar/tab_delimited/", "variant_summary.txt.gz"),
  overwrite = FALSE)

Arguments

url	The url to the ftp location of the clinvar dataset (tab delimited variant summary file) (e.g. ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz)
overwrite	default: FALSE, boolean value to decide if a fresh download should overwrite the existing file

Value

Path to the downloaded file

Examples

## Not run: 
#download
filePath <- getClinVarData()
#read first 100 lines
cv_head <- data.table::fread(text = readLines(filePath, n = 100))

## End(Not run)

BIMSBbioinfo/slimR documentation built on Nov. 4, 2021, 6:48 a.m.