diff --git a/DESCRIPTION b/DESCRIPTION index 5bd8131..a9b5fd2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: MungeSumstats Type: Package Title: Standardise summary statistics from GWAS -Version: 1.15.0 +Version: 1.15.1 Authors@R: c(person(given = "Alan", family = "Murphy", diff --git a/NEWS.md b/NEWS.md index caae33e..b0db8a3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +## CHANGES IN VERSION 1.15.1 + +### New features +*[FAQ Website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) added. +* Non-bi-allelic filter switched to FALSE by default in `format_sumstats()`. +Given the ever increasing number of non-bi-allelic SNPs in dbSNP, it no longer +makes sense to simply remove these. + ## CHANGES IN VERSION 1.13.7 ### Bug fix diff --git a/R/format_sumstats.R b/R/format_sumstats.R index 6f42374..ab0975f 100644 --- a/R/format_sumstats.R +++ b/R/format_sumstats.R @@ -151,8 +151,8 @@ #' not the P-value and so will be flipped i.e. default TRUE. #' @param allele_flip_frq Binary should the frequency (FRQ) column be flipped #' along with effect and z-score columns like Beta? Default TRUE. -#' @param bi_allelic_filter Binary Should non-biallelic SNPs be removed. Default -#' is TRUE. +#' @param bi_allelic_filter Binary Should non-bi-allelic SNPs be removed. +#' Default is TRUE. #' @param flip_frq_as_biallelic Binary Should non-bi-allelic SNPs frequency #' values be flipped as 1-p despite there being other alternative alleles? #' Default is FALSE but if set to TRUE, this allows non-bi-allelic SNPs to be diff --git a/README.Rmd b/README.Rmd index 74d1495..3acaf03 100644 --- a/README.Rmd +++ b/README.Rmd @@ -107,7 +107,10 @@ See the [OpenGWAS vignette website](https://al-murphy.github.io/MungeSumstats/ar for information on how to use MungeSumstats to access, standardise and perform quality control on GWAS Summary Statistics from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/). -If you have any problems please do file an [Issue](https://github.com/al-murphy/MungeSumstats/issues) here on GitHub. +Please read carefully through the [FAQ website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) +for an queries about running MungeSumstats. If you have any outside of this +problems please do file an [Issue](https://github.com/al-murphy/MungeSumstats/issues) +here on GitHub. # Future Enhancements diff --git a/README.md b/README.md index 5e002bf..9988d28 100644 --- a/README.md +++ b/README.md @@ -4,22 +4,22 @@ Authors: Alan Murphy, Brian Schilder and Nathan Skene
-Updated: Aug-07-2024 +Updated: Oct-30-2024
[![](https://img.shields.io/badge/release%20version-1.10.1-black.svg)](https://www.bioconductor.org/packages/MungeSumstats) -[![](https://img.shields.io/badge/devel%20version-1.13.4-black.svg)](https://github.com/neurogenomics/MungeSumstats) +[![](https://img.shields.io/badge/devel%20version-1.15.1-black.svg)](https://github.com/neurogenomics/MungeSumstats) [![](https://img.shields.io/github/last-commit/neurogenomics/MungeSumstats.svg)](https://github.com/neurogenomics/MungeSumstats/commits/master) -[![](https://img.shields.io/badge/download-19161/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats) +[![](https://img.shields.io/badge/download-21632/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats) [![License: Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0) [![](https://img.shields.io/badge/doi-https://doi.org/10.1093/bioinformatics/btab665-blue.svg)](https://doi.org/https://doi.org/10.1093/bioinformatics/btab665) - + # Introduction @@ -111,7 +111,10 @@ for information on how to use MungeSumstats to access, standardise and perform quality control on GWAS Summary Statistics from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/). -If you have any problems please do file an +Please read carefully through the [FAQ +website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) for an +queries about running MungeSumstats. If you have any outside of this +problems please do file an [Issue](https://github.com/al-murphy/MungeSumstats/issues) here on GitHub. diff --git a/man/check_allele_flip.Rd b/man/check_allele_flip.Rd index d536794..6958218 100644 --- a/man/check_allele_flip.Rd +++ b/man/check_allele_flip.Rd @@ -51,8 +51,8 @@ not the P-value and so will be flipped i.e. default TRUE.} \item{allele_flip_frq}{Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE.} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{flip_frq_as_biallelic}{Binary Should non-bi-allelic SNPs frequency values be flipped as 1-p despite there being other alternative alleles? diff --git a/man/check_bi_allelic.Rd b/man/check_bi_allelic.Rd index 24e183d..bc624b2 100644 --- a/man/check_bi_allelic.Rd +++ b/man/check_bi_allelic.Rd @@ -27,8 +27,8 @@ directly to MungeSumstats using the path parameter.} "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{log_folder_ind}{Binary Should log files be stored containing all filtered out SNPs (separate file per filter). The data is outputted in the diff --git a/man/check_dup_bp.Rd b/man/check_dup_bp.Rd index d817c29..d193c9b 100644 --- a/man/check_dup_bp.Rd +++ b/man/check_dup_bp.Rd @@ -18,8 +18,8 @@ check_dup_bp( ) } \arguments{ -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{check_dups}{whether to check for duplicates - if formatting QTL datasets this should be set to FALSE otherwise keep as TRUE. Default is TRUE.} diff --git a/man/check_dup_snp.Rd b/man/check_dup_snp.Rd index cd957e0..2fc0084 100644 --- a/man/check_dup_snp.Rd +++ b/man/check_dup_snp.Rd @@ -39,8 +39,8 @@ FALSE.} \item{log_files}{list of log file locations} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{check_dups}{whether to check for duplicates - if formatting QTL datasets this should be set to FALSE otherwise keep as TRUE. Default is TRUE.} diff --git a/man/check_no_allele.Rd b/man/check_no_allele.Rd index 196b180..d8c8916 100644 --- a/man/check_no_allele.Rd +++ b/man/check_no_allele.Rd @@ -53,8 +53,8 @@ FALSE.} \item{log_files}{list of log file locations} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{dbSNP}{version of dbSNP to be used for imputation (144 or 155).} } diff --git a/man/format_sumstats.Rd b/man/format_sumstats.Rd index 2490533..ce793f3 100644 --- a/man/format_sumstats.Rd +++ b/man/format_sumstats.Rd @@ -217,8 +217,8 @@ not the P-value and so will be flipped i.e. default TRUE.} \item{allele_flip_frq}{Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE.} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{flip_frq_as_biallelic}{Binary Should non-bi-allelic SNPs frequency values be flipped as 1-p despite there being other alternative alleles? diff --git a/man/import_sumstats.Rd b/man/import_sumstats.Rd index 88229dc..82ce66f 100644 --- a/man/import_sumstats.Rd +++ b/man/import_sumstats.Rd @@ -175,8 +175,8 @@ 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.} \item{\code{allele_flip_frq}}{Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE.} - \item{\code{bi_allelic_filter}}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} + \item{\code{bi_allelic_filter}}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{\code{flip_frq_as_biallelic}}{Binary Should non-bi-allelic SNPs frequency values be flipped as 1-p despite there being other alternative alleles? Default is FALSE but if set to TRUE, this allows non-bi-allelic SNPs to be diff --git a/man/validate_parameters.Rd b/man/validate_parameters.Rd index b57ab0e..a6b9294 100644 --- a/man/validate_parameters.Rd +++ b/man/validate_parameters.Rd @@ -158,8 +158,8 @@ not the P-value and so will be flipped i.e. default TRUE.} \item{allele_flip_frq}{Binary should the frequency (FRQ) column be flipped along with effect and z-score columns like Beta? Default TRUE.} -\item{bi_allelic_filter}{Binary Should non-biallelic SNPs be removed. Default -is TRUE.} +\item{bi_allelic_filter}{Binary Should non-bi-allelic SNPs be removed. +Default is TRUE.} \item{flip_frq_as_biallelic}{Binary Should non-bi-allelic SNPs frequency values be flipped as 1-p despite there being other alternative alleles? diff --git a/vignettes/MungeSumstats.Rmd b/vignettes/MungeSumstats.Rmd index 7d41868..6d33a11 100644 --- a/vignettes/MungeSumstats.Rmd +++ b/vignettes/MungeSumstats.Rmd @@ -171,6 +171,9 @@ to match LDSC (A1 will now be the effect allele). See more info on this [here](https://groups.google.com/g/ldsc_users/c/S7FZK743w68). Note that any effect columns (e.g. Z) will be inrelation to A1 now instead of A2. +Please read carefully through our [FAQ Website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) +to gain insight on how best to run MungeSumstats on your data. + # Data The *MungeSumstats* package contains small subsets of GWAS summary