validate_parameters {MungeSumstats} | R Documentation |
Ensure that the input parameters are logical
validate_parameters( path, ref_genome, convert_ref_genome, convert_small_p, compute_z, compute_n, convert_n_int, analysis_trait, INFO_filter, FRQ_filter, pos_se, effect_columns_nonzero, N_std, N_dropNA, rmv_chr, on_ref_genome, strand_ambig_filter, allele_flip_check, allele_flip_drop, allele_flip_z, allele_flip_frq, bi_allelic_filter, snp_ids_are_rs_ids, remove_multi_rs_snp, frq_is_maf, write_vcf, return_format, ldsc_format, imputation_ind, log_folder_ind, log_mungesumstats_msgs, mapping_file, tabix_index )
path |
Filepath for the summary statistics file to be formatted. A dataframe or datatable of the summary statistics file can also be passed directly to MungeSumstats using the path parameter. |
ref_genome |
name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data. |
convert_ref_genome |
name of the reference genome to convert to ("GRCh37" or "GRCh38"). This will only occur if the current genome build does not match. Default is not to convert the genome build (NULL). |
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. |
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. |
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 sumstats file). Default 0.9. |
FRQ_filter |
numeric The minimum value permissible of the frequency(FRQ) of the SNP (i.e. Allele Frequency (AF)) (if present in sumstats file). By default no filtering is done, i.e. value of 0. |
pos_se |
Binary Should the standard Error (SE) column be checked to ensure it is greater than 0? Those that are, are removed (if present in sumstats file). Default TRUE. |
effect_columns_nonzero |
Binary should the effect columns in the data BETA,OR (odds ratio),LOG_ODDS,SIGNED_SUMSTAT be checked to ensure no SNP=0. Those that do are removed(if present in sumstats file). Default FALSE. |
N_std |
numeric The number of standard deviations above the mean a SNP's N is needed to be removed. Default is 5. |
N_dropNA |
Drop rows where N is missing.Default is TRUE. |
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 checked against reference genome to infer if flipping is necessary. Default is TRUE. |
allele_flip_drop |
Binary Should the SNPs for which neither their A1 or A2 base pair values match a reference genome be dropped. Default is TRUE. |
allele_flip_z |
Binary should the Z-score be flipped along with effect and FRQ columns like Beta? It is assumed to be calculated off the effect size not the P-value and so will be flipped i.e. default TRUE. |
allele_flip_frq |
Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE. |
bi_allelic_filter |
Binary Should non-biallelic SNPs be removed. Default is TRUE. |
snp_ids_are_rs_ids |
Binary Should the supplied SNP ID's be assumed to be RSIDs. If not, imputation using the SNP ID for other columns like base-pair position or chromosome will not be possible. If set to FALSE, the SNP RS ID will be imputed from the reference genome if possible. Default is TRUE. |
remove_multi_rs_snp |
Binary Sometimes summary statistics can have multiple RSIDs on one row (i.e. related to one SNP), for example "rs5772025_rs397784053". This can cause an error so by default, the first RS ID will be kept and the rest removed e.g."rs5772025". If you want to just remove these SNPs entirely, set it to TRUE. Default is FALSE. |
frq_is_maf |
Conventionally the FRQ column is intended to show the minor/effect allele frequency (MAF) but sometimes the major allele frequency can be inferred as the FRQ column. This logical variable indicates that the FRQ column should be renamed to MAJOR_ALLELE_FRQ if the frequency values appear to relate to the major allele i.e. >0.5. By default this mapping won't occur i.e. is TRUE. |
write_vcf |
Whether to write as VCF (TRUE) or tabular file (FALSE). |
return_format |
If return_data is TRUE. Object type to be returned ("data.table","vranges","granges"). |
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 |
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. |
log_folder_ind |
Binary Should log files be stored containing all filtered out SNPs (separate file per filter). The data is outputted in the same format specified for the resulting sumstats file. The only exception to this rule is if output is vcf, then log file saved as .tsv.gz. Default is FALSE. |
log_mungesumstats_msgs |
Binary Should a log be stored containing all messages and errors printed by MungeSumstats in a run. Default is FALSE |
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 youf 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 data(sumstatsColHeaders) for default mapping and necessary format. |
tabix_index |
Index the formatted summary statistics with tabix for fast querying. |
No return