diff --git a/Makefile b/Makefile index 592354b..dc086ea 100644 --- a/Makefile +++ b/Makefile @@ -7,12 +7,12 @@ all: rd check clean rd: Rscript -e 'roxygen2::roxygenise(".")' -readme: +readme: rd Rscript -e 'rmarkdown::render("README.Rmd")' - Rscript -e 'pkgdown::build_site()' + Rscript -e 'pkgdown::build_site(examples=FALSE)' Rscript -e 'pkgdown::build_articles()' -readme2: +readme2: rd Rscript -e 'rmarkdown::render("README.Rmd", "html_document")' build: rd diff --git a/R/vcf-compare.R b/R/vcf-compare.R index 3aa6709..50a7f56 100644 --- a/R/vcf-compare.R +++ b/R/vcf-compare.R @@ -13,10 +13,10 @@ #' default c("DS", "GT") extracts 'DS' of the target and 'GT' of the truth. #' #' @param stats the statistics to be calculated. supports the following. -#' "r2": pearson correlation coefficient ** 2. -#' "f1": F1-score, good balance between sensitivity and precision. -#' "nrc": Non-Reference Concordance rate -#' "pse": Phasing Switch Error rate +#' "r2": the Pearson correlation coefficient square. +#' "f1": the F1-score, good balance between sensitivity and precision. +#' "nrc": the Non-Reference Concordance rate +#' "pse": the Phasing Switch Error rate #' #' @param by.sample logical. calculate sample-wise concordance, which can be stratified by MAF bin. #' @@ -41,6 +41,7 @@ #' @param ... options passed to \code{vcftable} #' #' @return a list of various statistics +#' #' @author Zilong Li \email{zilong.dk@gmail.com} #' #' @examples diff --git a/R/vcf-tables.R b/R/vcf-tables.R index aea8016..d50d543 100644 --- a/R/vcf-tables.R +++ b/R/vcf-tables.R @@ -20,6 +20,7 @@ #' e.g. "id01,id02", "^id01,id02". #' #' @param vartype restrict to specific type of variants. supports "snps","indels", "sv", "multisnps","multiallelics" +#' #' @param format the FORMAT tag to extract. default "GT" is extracted. #' #' @param ids character vector. restrict to sites with ID in the given vector. default NULL won't filter any sites. diff --git a/README.Rmd b/README.Rmd index 282e1b7..be42caf 100644 --- a/README.Rmd +++ b/README.Rmd @@ -93,15 +93,6 @@ par(mar=c(5,5,2,2), cex.lab = 2) vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b") ``` -```{r pse} -res <- vcfcomp(test = rawvcf, truth = phasedvcf, - stats = "pse", setid = TRUE, - region = "chr21:5000000-5500000", - samples = "HG00673,NA10840", - return_pse_sites = TRUE) -vcfplot(res, which=1:2, main = "Phasing switch error", ylab = "HG00673,NA10840") -``` - Check out the [vignettes](https://zilong-li.github.io/vcfppR/articles/) for more! ## `vcfsummary`: variants characterization diff --git a/README.md b/README.md index 5ca7287..8dde18f 100644 --- a/README.md +++ b/README.md @@ -104,18 +104,6 @@ vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b") -``` r -res <- vcfcomp(test = rawvcf, truth = phasedvcf, - stats = "pse", setid = TRUE, - region = "chr21:5000000-5500000", - samples = "HG00673,NA10840", - return_pse_sites = TRUE) -#> stats F1 or NRC or PSE only uses GT format -vcfplot(res, which=1:2, main = "Phasing switch error", ylab = "HG00673,NA10840") -``` - - - Check out the [vignettes](https://zilong-li.github.io/vcfppR/articles/) for more\! diff --git a/docs/404.html b/docs/404.html index 80e8a71..151a263 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,65 +8,52 @@ Page not found (404) • vcfppR - - - - + + + Skip to contents - -