A function to create a gwasglue2 SummarySet object from different sources and formats

Usage

create_summaryset(
  data,
  metadata = NULL,
  type = "tibble",
  qc = FALSE,
  beta_col = NULL,
  se_col = NULL,
  samplesize_col = NULL,
  pvalue_col = NULL,
  logpvalue_col = NULL,
  chr_col = NULL,
  position_col = NULL,
  rsid_col = NULL,
  effect_allele_col = NULL,
  other_allele_col = NULL,
  eaf_col = NULL,
  id_col = NULL,
  trait_col = NULL,
  build = NULL
)

Arguments

data

GWAS summary statistics.

metadata

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

type

Input @param data type. Default is "tibble". Other options: "vcf"

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 "beta" for @param type "tibble" and "ES"for @param type "vcf"..

se_col

Name of column with standard errors. The default is "se" for @param type "tibble" and "SE"for @param type "vcf".

samplesize_col

Column name for sample size. The default is "n" for @param type "tibble" and "SS"for @param type "vcf".

pvalue_col

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

logpvalue_col

Name of column with log(p-value). The default is "LP" for @param type "vcf".

chr_col

Column name for chromosome . The default is "chr" for @param type "tibble" and "seqnames"for @param type "vcf".

position_col

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

rsid_col

Required name of column with variants rs IDs. The default is "rsid" for @param type "tibble" and "ID"for @param type "vcf".

effect_allele_col

Name of column with effect allele. Must contain only the characters "A", "C", "T" or "G". The default is "ea" for @param type "tibble" and "ALT"for @param type "vcf".

other_allele_col

Name of column with non effect allele. Must contain only the characters "A", "C", "T" or "G". The default is "nea for @param type "tibble" and "REF"for @param type "vcf".

eaf_col

Name of column with effect allele frequency. The default is "eaf" for @param type "tibble" and "AF"for @param type "vcf".

id_col

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

trait_col

Column name for the column with phenotype name corresponding the the variant. The default is "trait"

build

Reference genome assembly to generate the genomic data. 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 different sources and formats

Usage

Arguments

Value

See also