Merge pull request #31 from remlapmot/rita-plus-tp

Suggested additional fixes
MRCIEU · Sep 4, 2023 · 9da6597 · 9da6597
2 parents 39f5d2f + 8c49368
commit 9da6597
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,8 +6,8 @@ Authors@R: c(
            comment = c(ORCID = "0000-0003-0920-1055")),
     person("Tom", "Palmer", , "tom.palmer@bristol.ac.uk", role = "ctb",
            comment = c(ORCID = "0000-0003-4655-4511")),
-  person("Rita", "Rasteiro", email="rita.rasteiro@bristol.ac.uk", role = c("ctb"),
-            comment=c(ORCID = "0000-0002-4217-3060"))
+    person("Rita", "Rasteiro", , "rita.rasteiro@bristol.ac.uk", role = "ctb",
+           comment = c(ORCID = "0000-0002-4217-3060"))
   )
 Description: Tools for dealing with GWAS summary data in VCF format.
     Includes reading, querying, writing, as well as helper functions such
@@ -25,6 +25,7 @@ Imports:
     genetics.binaRies,
     GenomeInfoDb,
     GenomicRanges,
+    gwasglue2,
     IRanges,
     magrittr,
     RCurl,
@@ -35,8 +36,7 @@ Imports:
     stringr,
     SummarizedExperiment,
     utils,
-    VariantAnnotation,
-    gwasglue2
+    VariantAnnotation
 Suggests: 
     knitr,
     rmarkdown,
@@ -47,5 +47,6 @@ Remotes:
     github::mrcieu/genetics.binaRies,
     github::mrcieu/gwasglue2
 Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 SystemRequirements: GNU unzip
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,4 @@
 # gwasvcf 0.1.2
-(Release date: 10-08-2023)
 
-* New gwasvcf_to_summaryset function to create a [gwasglue2](https://mrcieu.github.io/gwasglue2) Summaryset object from a vcf file
-* Fixed error in get_ld_proxies related with argument validate, deprecated in as_tibble() (tibble 2.0.0)
-
+* New `gwasvcf_to_summaryset()` function to create a [gwasglue2](https://mrcieu.github.io/gwasglue2) SummarySet object from a vcf file
+* Fixed error in `get_ld_proxies()` related with argument `validate`, deprecated in `as_tibble()` (tibble 2.0.0)
diff --git a/R/gwasglue.R b/R/gwasglue.R
@@ -5,7 +5,7 @@
 #' Create a SummarySet
 #' 
 #' Returns a gwasglue2 SummarySet object
-#' @param vcf Path or URL to GWAS-VCF file or VCF object e.g. output from VariantAnnotation::readVcf, gwasvcftools::query_vcf or [query_gwas()]
+#' @param vcf Path or URL to GWAS-VCF file or VCF object e.g. output from [VariantAnnotation::readVcf()], [create_vcf()] or [query_gwas()]
 #' @export
 gwasvcf_to_summaryset <- function(vcf){
 	# get metadata from vcf and create metadata object
@@ -19,4 +19,3 @@ gwasvcf_to_summaryset <- function(vcf){
 
     return(s)
 }
-
diff --git a/R/pval_index.r b/R/pval_index.r
@@ -1,6 +1,6 @@
 #' Create pval index from GWAS-VCF file
 #'
-#' Create a separate file called <id>.pvali which is used to speed up p-value queries
+#' Create a separate file called `<id>.pvali` which is used to speed up p-value queries.
 #'
 #' @param vcffile VCF filename
 #' @param maximum_pval Maximum p-value to include. Default = 0.05

diff --git a/R/query.r b/R/query.r
@@ -2,7 +2,7 @@
 #'
 #' Read in GWAS summary data with filters on datasets (if multiple datasets per file) and/or chromosome/position, rsids or pvalues. Chooses most optimal choice for the detected operating system. Typically chrompos searches are the fastest. On Windows, rsid or pvalue filters from a file will be slow. 
 #'
-#' @param vcf Path or URL to GWAS-VCF file or VCF object e.g. output from VariantAnnotation::readVcf or gwasvcftools::query_vcf
+#' @param vcf Path or URL to GWAS-VCF file or VCF object e.g. output from [VariantAnnotation::readVcf()] or [create_vcf()]
 #' @param chrompos Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns `chrom`, `start`, `end`.
 #' @param rsid Vector of rsids
 #' @param pval  P-value threshold (NOT -log10)

diff --git a/man/create_pval_index_from_vcf.Rd b/man/create_pval_index_from_vcf.Rd
diff --git a/man/gwasvcf_to_summaryset.Rd b/man/gwasvcf_to_summaryset.Rd
diff --git a/man/parse_chrompos.Rd b/man/parse_chrompos.Rd
diff --git a/man/query_chrompos_bcftools.Rd b/man/query_chrompos_bcftools.Rd
diff --git a/man/query_chrompos_file.Rd b/man/query_chrompos_file.Rd
diff --git a/man/query_chrompos_vcf.Rd b/man/query_chrompos_vcf.Rd
diff --git a/man/query_gwas.Rd b/man/query_gwas.Rd
diff --git a/man/vcflist_overlaps.Rd b/man/vcflist_overlaps.Rd
diff --git a/vignettes/guide.Rmd b/vignettes/guide.Rmd
@@ -347,7 +347,7 @@ You may want to first harmonise the data so that all the non-effect alleles are
 
 Although still under development, if compared with its predecessor, the [gwasglue2](https://mrcieu.github.io/gwasglue2/) package has several new features, including the use of S4 R objects.
 
-It is possible to create a `SummarySet` object from a GWAS-VCF file or VCF object e.g. output from `VariantAnnotation::readVcf()`, `gwasvcftools::query_vcf()` or `query_gwas()` using the `gwasvcf_to_summaryset()` function.
+It is possible to create a `SummarySet` object from a GWAS-VCF file or VCF object e.g. output from `VariantAnnotation::readVcf()`, `create_vcf()` or `query_gwas()` using the `gwasvcf_to_summaryset()` function.
 
 
 For example:
@@ -358,4 +358,3 @@ summaryset <- readVcf(vcffile) %>%
 ```
 
 Once the `SummarySet` objects are created, it is possible to use `gwasglue2` to harmonise data, harmonise against a LD matrix, remap genomic coordinates to a different genome assembly, convert to other formats and more.
-