SNPedia.R

if (!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install()


if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("BiocStyle", version = "3.8")


## ----style, echo = FALSE, results = 'asis'---------------------------------
BiocStyle::markdown()

## --------------------------------------------------------------------------
library (SNPediaR)
pg <- getPages (titles = "Rs53576")
pg

## --------------------------------------------------------------------------
pgs <- getPages (titles = c ("Rs53576(A;A)", "Rs53576(A;G)", "Rs53576(G;G)"))
pgs

## --------------------------------------------------------------------------
extractSnpTags (pg$Rs53576)

## --------------------------------------------------------------------------
sapply (pgs, extractGenotypeTags)

## --------------------------------------------------------------------------
getPages (titles = c ("Rs53576(A;A)", "Rs53576(A;G)", "Rs53576(G;G)"),
          wikiParseFunction = extractGenotypeTags,
          tags = c ("allele1", "allele2", "magnitude"))

## --------------------------------------------------------------------------
findPMID <- function (x) {
  x <- unlist (strsplit (x, split = "\n"))
  x <- grep ("PMID=", x, value = TRUE)
  x
}

## --------------------------------------------------------------------------
getPages (titles = c ("Rs53576", "Rs1815739"),
          wikiParseFunction = findPMID)


## --------------------------------------------------------------------------
res <- getCategoryElements (category = "Is_a_medical_condition")
head (res)

## --------------------------------------------------------------------------
grep ('cancer', res, value = TRUE)

## --------------------------------------------------------------------------
sessionInfo ()