check_range_p_val: Ensure that the p values are not >1 and if so set to 1

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure that the p values are not >1 and if so set to 1

Description

Ensure that the p values are not >1 and if so set to 1

Usage

check_range_p_val(sumstats_dt, convert_large_p, convert_neg_p, imputation_ind)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS
convert_large_p	Binary, should p-values >1 be converted to 1? P-values >1 should not be possible and can cause errors with LDSC/MAGMA and should be converted. Default is TRUE.
convert_neg_p	Binary, should p-values <0 be converted to 0? Negative p-values should not be possible 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). On the flipped value, this denoted whether the alelles where switched based on MungeSumstats initial choice of A1, A2 from the input column headers and thus may not align with what the creator intended.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

Source

sumstats_dt <- MungeSumstats:::formatted_example() sumstats_dt$P[1:3] <- 5 sumstats_dt$P[6:10] <- -5 sumstats <- check_range_p_val(sumstats_dt = sumstats_dt, convert_large_p = TRUE, convert_neg_p = TRUE, imputation_ind = TRUE)

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.