Creates a DataSet object using GWAS summary statistics, and harmonise data against data

Usage

create_dataset_from_tibble(
  data = list(),
  metadata = NULL,
  harmonise = TRUE,
  tolerance = 0.08,
  action = 1,
  beta_col = "beta",
  se_col = "se",
  samplesize_col = "n",
  pvalue_col = "p",
  chr_col = "chr",
  position_col = "position",
  rsid_col = "rsid",
  effect_allele_col = "ea",
  other_allele_col = "nea",
  eaf_col = "eaf",
  id_col = "id",
  trait_col = "trait",
  ...
)

Arguments

data

A list of GWAS summary data (tibles)

metadata

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

harmonise

logical (default TRUE). It harmonises the summary sets in the DataSet against each other.

tolerance

Inherited from harmoniseData() (default 0.08)

action

Inherited from harmoniseData() (Default 1)

action = 1: Assume all alleles are coded on the forward strand, i.e. do not attempt to flip alleles
action = 2: Try to infer positive strand alleles, using allele frequencies for palindromes (default, conservative);
action = 3: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis (more conservative).

beta_col

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

se_col

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

samplesize_col

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

pvalue_col

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

chr_col

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

position_col

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

rsid_col

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

effect_allele_col

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

other_allele_col

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

eaf_col

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

id_col

The default is "id".

trait_col

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

...

Other columns

Value

A harmonised gwasglue2 DataSet object

Creates a DataSet object using GWAS summary statistics, and harmonise data against data

Usage

Arguments

Value

See also