Add FAQ website

Al-Murphy · Oct 30, 2024 · b3c0cf4 · b3c0cf4
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -4,22 +4,22 @@
 <i>Authors</i>: Alan Murphy, Brian Schilder and Nathan Skene  
 </h5>
 <h5>  
-<i>Updated</i>: Aug-07-2024  
+<i>Updated</i>: Oct-30-2024  
 </h5>
 
 <!-- Readme.md is generated from Readme.Rmd. Please edit that file -->
 <!-- badges: start -->
 
 [![](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)
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-[![](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)
 <!-- badges: end -->
 <!--[![R build status](https://github.com/neurogenomics/MungeSumstats/workflows/rworkflows/badge.svg)](https://github.com/neurogenomics/MungeSumstats/actions)-->
-<!--`[![](https://codecov.io/gh/neurogenomics/MungeSumstats/branch/master/graph/badge.svg)](https://codecov.io/gh/neurogenomics/MungeSumstats) -->
+<!--`[![](https://codecov.io/gh/neurogenomics/MungeSumstats/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/MungeSumstats) -->
 
 # 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
diff --git a/man/check_bi_allelic.Rd b/man/check_bi_allelic.Rd
diff --git a/man/check_dup_bp.Rd b/man/check_dup_bp.Rd
diff --git a/man/check_dup_snp.Rd b/man/check_dup_snp.Rd
diff --git a/man/check_no_allele.Rd b/man/check_no_allele.Rd
diff --git a/man/format_sumstats.Rd b/man/format_sumstats.Rd
diff --git a/man/import_sumstats.Rd b/man/import_sumstats.Rd
diff --git a/man/validate_parameters.Rd b/man/validate_parameters.Rd
diff --git 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