A function to create a gwasglue2 SummarySet object from a vcf file

Usage

create_summaryset_from_gwasvcf(
  data,
  metadata = NULL,
  qc = FALSE,
  beta_col = "ES",
  se_col = "SE",
  samplesize_col = "SS",
  logpvalue_col = "LP",
  pvalue_col = "p",
  chr_col = "seqnames",
  position_col = "start",
  rsid_col = "ID",
  effect_allele_col = "ALT",
  other_allele_col = "REF",
  eaf_col = "AF",
  id_col = "id",
  build = NULL
)

Arguments

data

GWAS summary statistics. In the GWAS vcf dataframe format

metadata

A list with metadata information. If NULL, it creates metadata with information retrieved from the dataset

qc

Quality control. It checks the @param data and look for problems that can stop gwasglue2 from runing. If TRUE gwasglue will try to solve the problems. Default is FALSE

beta_col

Name of column with effect sizes. The default is "ES".

se_col

Name of column with standard errors. The default is "SE".

samplesize_col

Column name for sample size. The default is "SS".

logpvalue_col

Name of column with log(p-value). The default is "LP".

pvalue_col

Name of column with p-value. The default is "p".

chr_col

Column name for chromosome . The default is "seqnames".

position_col

Column name for the position. Together, with @param chr gives the physical coordinates of the variant. The default is "start".

rsid_col

Required name of column with variants rs IDs. The default is "ID".

effect_allele_col

Name of column with effect allele. Must contain only the characters "A", "C", "T" or "G". The default is "ALT".

other_allele_col

Name of column with non effect allele. Must contain only the characters "A", "C", "T" or "G". The default is "REF".

eaf_col

Name of column with effect allele frequency. The default is "AF".

id_col

GWAS study ID column. The default is "id".

build

Reference genome assembly to generate the vcf file. Default is NULL.

Options are "NCBI34", "NCBI35", "NCBI36", "GRCh37" or "GRCh38".

Value

A gwasglue2 SummarySet object

A function to create a gwasglue2 SummarySet object from a vcf file

Usage

Arguments

Value

See also