infer_effect_column: Infer if effect relates to a1 or A2 if ambiguously named

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Infer if effect relates to a1 or A2 if ambiguously named

Description

Three checks are made to infer which allele the effect/frequency information relates to if they are ambiguous (named A1 and A2 or equivalent):

1. Check if ambiguous naming conventions are used (i.e. allele 1 and 2 or equivalent). If not exit, otherwise continue to next checks. This can be checked by using the mapping file and splitting A1/A2 mappings by those that contain 1 or 2 (ambiguous) or doesn't contain 1 or 2 e.g. effect, tested (unambiguous so fine for MSS to handle as is).

2. Look for effect column/frequency column where the A1/A2 explicitly mentioned, if found then we know the direction and should update A1/A2 naming so A2 is the effect column. We can look for such columns by getting every combination of A1/A2 naming and effect/frq naming.

3. If not found in 2, a final check should be against the reference genome, whichever of A1 and A2 has more of a match with the reference genome should be taken as not the effect allele. There is an assumption in this but is still better than guessing the ambiguous allele naming.

Usage

infer_effect_column(
  sumstats_dt,
  dbSNP = 155,
  sampled_snps = 10000,
  mapping_file = sumstatsColHeaders,
  nThread = nThread,
  ref_genome = NULL,
  on_ref_genome = TRUE,
  infer_eff_direction = TRUE,
  return_list = TRUE
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS.
dbSNP	version of dbSNP to be used for imputation (144 or 155).
sampled_snps	Downsample the number of SNPs used when inferring genome build to save time.
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.
nThread	Number of threads to use for parallel processes.
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.
infer_eff_direction	Binary Should a check take place to ensure the alleles match the effect direction? Default is TRUE.
return_list	Return the sumstats_dt within a named list (default: TRUE).

Value

list containing sumstats_dt, the modified summary statistics data table object

Examples

sumstats <- MungeSumstats::formatted_example()
#for speed, don't run on_ref_genome part of check (on_ref_genome = FALSE)
sumstats_dt2<-infer_effect_column(sumstats_dt=sumstats,on_ref_genome = FALSE)

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