get_genome_build {MungeSumstats} | R Documentation |
Infers the genome build of the summary statistics file (GRCh37 or GRCh38) from the data. Uses SNP (RSID) & CHR & BP to get genome build.
get_genome_build( sumstats, nThread = 1, sampled_snps = 10000, standardise_headers = TRUE, mapping_file = sumstatsColHeaders, header_only = FALSE )
sumstats |
data table/data frame obj of the summary statistics file for the GWAS ,or file path to summary statistics file. |
nThread |
Number of threads to use for parallel processes. |
sampled_snps |
Downsample the number of SNPs used when inferring genome build to save time. |
standardise_headers |
Run
|
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 your 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
|
header_only |
Instead of reading in the entire |
ref_genome the genome build of the data