update pkgdown

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

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

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.

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

README.md

@@ -104,18 +104,6 @@ vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 
 <img src="man/figures/README-r2-1.png" width="100%" />
 
-``` 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")
-```
-
-<img src="man/figures/README-pse-1.png" width="100%" />
-
 Check out the [vignettes](https://zilong-li.github.io/vcfppR/articles/)
 for more\!