check_small_p_val {MungeSumstats}R Documentation

Ensure that the p values are not 5e-324 or lower, if so set to 0

Description

Ensure that the p values are not 5e-324 or lower, if so set to 0

Usage

check_small_p_val(sumstats_dt, path, convert_small_p, imputation_ind)

Arguments

sumstats_dt

data table obj of the summary statistics file for the GWAS

path

Filepath for the summary statistics file to be formatted

convert_small_p

Binary, should p-values < 5e-324 be converted to 0? Small p-values pass the R limit and can cause errors with LDSC/MAGMA and should be converted. Default is TRUE.

imputation_ind

Binary Should a column be added for each imputation step to show what SNPs have imputed values for differing fields. This includes a field denoting SNP allele flipping (flipped). Note these columns will be in the formatted summary statistics returned. Default is FALSE.

Value

list containing sumstats_dt, the modified summary statistics data table object


[Package MungeSumstats version 1.2.2 Index]