check_on_ref_genome: Ensure all SNPs are on the reference genome

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure all SNPs are on the reference genome

Description

Ensure all SNPs are on the reference genome

Usage

check_on_ref_genome(
  sumstats_dt,
  path,
  ref_genome,
  on_ref_genome,
  indels = indels,
  rsids,
  imputation_ind,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files,
  dbSNP
)

Arguments

path	Filepath for the summary statistics file to be formatted. A dataframe or datatable of the summary statistics file can also be passed directly to MungeSumstats using the path parameter.
ref_genome	name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.
on_ref_genome	Binary Should a check take place that all SNPs are on the reference genome by SNP ID. Default is TRUE.
indels	Binary does your Sumstats file contain Indels? These don't exist in our reference file so they will be excluded from checks if this value is TRUE. Default is TRUE.
imputation_ind	Binary Should a column be added for each imputation step to show what SNPs have imputed values for differing fields. This includes a field denoting SNP allele flipping (flipped). On the flipped value, this denoted whether the alelles where switched based on MungeSumstats initial choice of A1, A2 from the input column headers and thus may not align with what the creator intended.Note these columns will be in the formatted summary statistics returned. Default is FALSE.
log_folder_ind	Binary Should log files be stored containing all filtered out SNPs (separate file per filter). The data is outputted in the same format specified for the resulting sumstats file. The only exception to this rule is if output is vcf, then log file saved as .tsv.gz. Default is FALSE.
tabix_index	Index the formatted summary statistics with tabix for fast querying.
nThread	Number of threads to use for parallel processes.
log_files	list of log file locations
dbSNP	version of dbSNP to be used for imputation (144 or 155).

Value

A list containing two data tables:

• sumstats_dt : the modified summary statistics data table object

• rsids : snpsById, filtered to SNPs of interest if loaded already. Or else NULL

• log_files : log file list

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.