check_ldsc_format {MungeSumstats} | R Documentation |
Format summary statistics for direct input to
Linkage Disequilibrium SCore (LDSC) regression without the need
to use their munge_sumstats.py
script first.
check_ldsc_format( sumstats_dt, ldsc_format, convert_n_int, allele_flip_check, compute_z, compute_n )
sumstats_dt |
data table obj of the summary statistics file for the GWAS. |
ldsc_format |
Binary Ensure that output format meets all requirements to be fed directly into LDSC without the need for additional munging. Default is FALSE |
convert_n_int |
Binary, if N (the number of samples) is not an integer, should this be rounded? Default is TRUE. |
allele_flip_check |
Binary Should the allele columns be checked against reference genome to infer if flipping is necessary. Default is TRUE. |
compute_z |
Whether to compute Z-score column from P. Default is FALSE. Note that imputing the Z-score for every SNP will not correct be perfectly correct and may result in a loss of power. This should only be done as a last resort. |
compute_n |
Whether to impute N. Default of 0 won't impute, any other integer will be imputed as the N (sample size) for every SNP in the dataset. Note that imputing the sample size for every SNP is not correct and should only be done as a last resort. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one of these for this field or a vector of multiple. Sum and an integer value creates an N column in the output whereas giant, metal or ldsc create an Neff or effective sample size. If multiples are passed, the formula used to derive it will be indicated. |
Formatted summary statistics