Download a Bioconductor vignette

The actual vignette path is available using biocPkgList.

getBiocVignette(
  vignettePath,
  destfile = tempfile(),
  version = BiocManager::version()
)

Arguments

vignettePath

character(1) the additional path information to get to the vignette

destfile

character(1) the file location to store the vignette

version

character(1) such as "3.7", defaults to user version

Value

character(1) The filename of the downloaded vignette

Examples

x = biocPkgList()
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cloud.r-project.org
tmp = getBiocVignette(x$vignettes[[1]][1])
tmp
#> [1] "/tmp/RtmpBiSyxe/file23321543153f"

if (FALSE) {
library(pdftools)
y = pdf_text(tmp)
y = paste(y,collapse=" ")
library(tm)
v = VCorpus(VectorSource(y))
library(magrittr)

v <- v %>%
    tm_map(stripWhitespace) %>%
    tm_map(content_transformer(tolower)) %>%
    tm_map(removeWords, stopwords("english")) %>%
    tm_map(stemDocument)
dtm = DocumentTermMatrix(v)
inspect(DocumentTermMatrix(v,
    list(dictionary = as.character(x$Package))))
}