Standardise the column headers in the Summary Statistics files

Use a reference data table of common column header names (stored in sumstatsColHeaders or user inputted mapping file) to convert them to a standard set, i.e. chromosome -> CHR. This function does not check that all the required column headers are present. The amended header is written directly back into the file

standardise_header(
  sumstats_dt,
  mapping_file = sumstatsColHeaders,
  uppercase_unmapped = TRUE,
  return_list = TRUE
)

Arguments

sumstats_dt

data table obj of the summary statistics file for the GWAS.

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.

uppercase_unmapped

For columns that could not be identified in the mapping_file, return them in the same format they were input as (without forcing them to uppercase).

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_dt <- data.table::fread(system.file("extdata", "eduAttainOkbay.txt",
                                             package = "MungeSumstats"))
sumstats_dt2 <- standardise_header(sumstats_dt=sumstats_dt)
#> Standardising column headers.
#> First line of summary statistics file: 
#> MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval