check_allele_flip: Ensure A1 & A2 are correctly named, if GWAS SNP constructed...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure A1 & A2 are correctly named, if GWAS SNP constructed as Alternative/Reference or Risk/Nonrisk alleles these SNPs will need to be converted to Reference/Alternative or Nonrisk/Risk. Here non-risk is defined as what's on the reference genome (this may not always be the case).

Description

Ensure A1 & A2 are correctly named, if GWAS SNP constructed as Alternative/Reference or Risk/Nonrisk alleles these SNPs will need to be converted to Reference/Alternative or Nonrisk/Risk. Here non-risk is defined as what's on the reference genome (this may not always be the case).

Usage

check_allele_flip(
  sumstats_dt,
  path,
  ref_genome,
  rsids,
  allele_flip_check,
  allele_flip_drop,
  allele_flip_z,
  allele_flip_frq,
  bi_allelic_filter,
  flip_frq_as_biallelic,
  imputation_ind,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files,
  standardise_headers = FALSE,
  mapping_file,
  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.
allele_flip_check	Binary Should the allele columns be checked against reference genome to infer if flipping is necessary. Default is TRUE.
allele_flip_drop	Binary Should the SNPs for which neither their A1 or A2 base pair values match a reference genome be dropped. Default is TRUE.
allele_flip_z	Binary should the Z-score be flipped along with effect and FRQ columns like Beta? It is assumed to be calculated off the effect size not the P-value and so will be flipped i.e. default TRUE.
allele_flip_frq	Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE.
bi_allelic_filter	Binary Should non-biallelic SNPs be removed. Default is TRUE.
flip_frq_as_biallelic	Binary Should non-bi-allelic SNPs frequency values be flipped as 1-p despite there being other alternative alleles? Default is FALSE but if set to TRUE, this allows non-bi-allelic SNPs to be kept despite needing flipping.
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
standardise_headers	Run standardise_sumstats_column_headers_crossplatform first.
mapping_file	MungeSumstats has a pre-defined column-name mapping file which should cover the most common column headers and their interpretations. However, if a column header that is in youf file is missing of the mapping we give is incorrect you can supply your own mapping file. Must be a 2 column dataframe with column names "Uncorrected" and "Corrected". See data(sumstatsColHeaders) for default mapping and necessary format.
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.