List of uncorrected column headers often found in GWAS Summary Statistics column headers. Note the effect allele will always be the A2 allele, this is the approach done for VCF(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805039/). This is enforced with the column header corrections here and also the check allele flipping test.

data("sumstatsColHeaders")

Format

dataframe with 2 columns

Source

The code to prepare the .Rda file file from the marker file is: # Most the data in the below table comes from the LDSC github wiki data("sumstatsColHeaders") # Make additions to sumstatsColHeaders using github version of MungeSumstats- # shown is an example of adding columns for Standard Error (SE) #se_cols <- data.frame("Uncorrected"=c("SE","se","STANDARD.ERROR", # "STANDARD_ERROR","STANDARD-ERROR"), # "Corrected"=rep("SE",5)) #sumstatsColHeaders <- rbind(sumstatsColHeaders,se_cols) #Once additions are made, order & save the new mapping dataset #now sort ordering -important for logic that # uncorrected=corrected comes first sumstatsColHeaders$ordering <- sumstatsColHeaders$Uncorrected==sumstatsColHeaders$Corrected sumstatsColHeaders <- sumstatsColHeaders[order(sumstatsColHeaders$Corrected, sumstatsColHeaders$ordering,decreasing = TRUE),] rownames(sumstatsColHeaders)<-1:nrow(sumstatsColHeaders) sumstatsColHeaders$ordering <- NULL #manually move FRWQUENCY to above MAR - github issue 95 frequency <- sumstatsColHeaders[sumstatsColHeaders$Uncorrected=="FREQUENCY",] maf <- sumstatsColHeaders[sumstatsColHeaders$Uncorrected=="MAF",] if(as.integer(rownames(frequency))>as.integer(rownames(maf))){ sumstatsColHeaders[as.integer(rownames(frequency)),] <- maf sumstatsColHeaders[as.integer(rownames(maf)),] <- frequency } usethis::use_data(sumstatsColHeaders,overwrite = TRUE, internal=TRUE) save(sumstatsColHeaders, file="data/sumstatsColHeaders.rda") # You will need to restart your r session for effects to take account