GWAS_data_reader: GWAS_data_reader

In LucaAnholt/PanViz: Integrating Multi-Omic Network Data With Summay-Level GWAS Data

GWAS_data_reader

Description

GWAS_data_reader

Usage

GWAS_data_reader(file, snp_col, study_col, trait_col)

Arguments

file	- Character (string) containing the directory path to a .tsv or .csv file containing summary level GWAS data, typically this can be sourced from major GWAS databases such as the GWAS Catalog or GWAS Central.
snp_col	- Character (string) reflecting the column name containing the SNP (standard dbSNP accession number, e.g. rs992531) data. In data sourced from the GWAS Catalog, this column will typically be named "SNPS" and in GWAS Central this will typically be "Source Marker Accession".
study_col	- Character (string) reflecting the column name containing the study names associated with each SNP. In data sourced from the GWAS Catalog, this column will typically be named "STUDY" and in GWAS Central this will typically be "Study Name".
trait_col	- Character (string) reflecting the column name containing the trait/phenotype names associated with each SNP. In data sourced from the GWAS Catalog, this column will typically be named "DISEASE/TRAIT" and in GWAS Central this will typically be "Annotation Name".

Value

A processed dataframe containing only the columns including GWAS studies, traits/phenotypes and relevant SNPs in NCBI standard accession number naming convention

Examples

##getting directory path to GWAS Catalog association .tsv file:
path = system.file("extdata",
  "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv",
  package="PanViz")
##opening/cleaning data:
df <- PanViz::GWAS_data_reader(file = path,
  snp_col = "SNPS",
  study_col = "STUDY",
  trait_col = "DISEASE/TRAIT")
##getting directory path to GWAS Central association .tsv file:
path = system.file("extdata", "GWASCentralMart_ERplusBC.tsv",
  package="PanViz")
##opening/cleaning data:
df <- PanViz::GWAS_data_reader(file = path,
  snp_col = "Source Marker Accession",
  study_col = "Study Name",
  trait_col = "Annotation Name")

LucaAnholt/PanViz documentation built on April 17, 2022, 7:28 a.m.