validate_parameters {MungeSumstats} | R Documentation |
Ensure that the input parameters are logical
validate_parameters( path, ref_genome, convert_small_p, convert_n_int, analysis_trait, INFO_filter, N_std, rmv_chr, on_ref_genome, strand_ambig_filter, allele_flip_check, bi_allelic_filter )
path |
Filepath for the summary statistics file to be formatted |
ref_genome |
name of the reference genome used for the GWAS (GRCh37 or GRCh38) |
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. |
convert_n_int |
Binary, if N (the number of samples) is not an integer, should this be rounded? Default is TRUE. |
analysis_trait |
If multiple traits were studied, name of the trait for analysis from the GWAS. Default is NULL |
INFO_filter |
numeric The minimum value permissible of the imputation information score (if present in sumstatsfile). Default 0.9 |
N_std |
numeric The number of standard deviations above the mean a SNP's N is needed to be removed. Default is 5. |
rmv_chr |
vector or character The chromosomes on which the SNPs should be removed. Use NULL if no filtering necessary. Default is X, Y and mitochondrial. |
on_ref_genome |
Binary Should a check take place that all SNPs are on the reference genome by SNP ID. Default is TRUE |
strand_ambig_filter |
Binary Should SNPs with strand-ambiguous alleles be removed. Default is FALSE |
allele_flip_check |
Binary Should the allele columns be chacked against reference genome to infer if flipping is necessary. Default is TRUE |
bi_allelic_filter |
Binary Should non-biallelic SNPs be removed. Default is TRUE |
No return