Package 'SNPediaR'

Extract information form downloaded SNPedia pages.

Description

SNPedia pages usually have a table in the right hand side which summarizes most relevant information in the page. This functions help extracting this kind of information for the given tags or rows.

Usage

extractTags (x, tags)
extractSnpTags (x, tags)
extractGenotypeTags (x, tags)

Arguments

x	a wiki page (single character vector)
tags	character vector of tags (row names) to be collected.

Details

extractTags is a general purpose function aimed to work at any page. extractSnpTags calls extractTags with a set of predefined tags suitable for SNP pages. extractGenotypeTags does the same for genotype pages.

This functions take a character vector of length one but return a vector with as many values as the tag list provided. They are devised to be used with sapply functions.

Notice that in SNPedia not all information presented in the HTML table is available in the JSON format retrieved by the R package. Risk information for instance needs to be collected from the genotype pages as it is not available in the JSON version of the SNP pages.

Value

A character vector with the value of each of the tags if available in the page and NA otherwise.

See Also

getPages, getCategoryElements

Examples

res <- getPages (c ("Rs1234", "Rs53576"))
t (sapply (res, extractSnpTags))

extractTags (res[[1]], tags = c("rsid", "Chromosome", "position"))

res <- getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"))
t (sapply (res, extractGenotypeTags))

getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"),
          wikiParseFunction = extractGenotypeTags)

getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"),
          wikiParseFunction = extractGenotypeTags,
          tags = c("rsid", "allele1", "allele2"))

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Get all elements of a given category

Description

A function to get all page names of SNPedia tagged under the indicated category.

Usage

getCategoryElements(category, verbose = FALSE, includeTemplates = FALSE,
  limit, baseURL, format, query, continue)

Arguments

category	The category to be used. Just one at a time.
verbose	If TRUE some messages are provided.
includeTemplates	If TRUE page templates are kept in the output.
limit	The maximum number of items to be queried at a time.
baseURL	SNPedia boots URL.
format	Downloading format. Currently just JSON is available.
query	The query to be iterated.
continue	To be used in multi-page queries.

Details

A list of all available categories may be found at:

http://www.snpedia.com/index.php/Special:Categories

Most used categories are:

• Is_a_medical_condition

• Is_a_medical_condition

• Is_a_medicine

• Is_a_topic

• Is_a_snp

• In_dbSNP

• Is_a_genotype

Some template pages are included in their corresponding category. By default those will be removed. Set includeTemplates to TRUE is you want to keep them.

Parameters other than category and verbose are not intended for standard users.

Value

A character vector containing the names of the pages under the required category.

See Also

getPages, extractTags

Examples

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

## Not run: 
res <- getCategoryElements(category = "Is_a_snp")

## End(Not run)

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Download SNPedia pages

Description

A function to download the (wiki) text content of a list of SNPedia pages.

Usage

getPages(titles, verbose = FALSE, limit = 50,
  wikiParseFunction = identity, baseURL, format, query, ...)

Arguments

titles	Titles of the pages to be downloaded.
verbose	If TRUE some messages are provided.
limit	The maximum number of items to be queried at a time.
wikiParseFunction	Function to be used to parse the wiki code at downloading time. Default is identity so the raw wiki text is provided.
baseURL	SNPedia boots URL.
format	Downloading format. Currently just JSON is available.
query	The query to be iterated.
...	any parameter to be pasted to the wikiParseFunction.

Details

JSON format is parsed to extract the wiki text returned by the function.

If the wikiParseFunction parameter is provided, parsing of the pages is done internally once each batch of pages is downloaded.

Pages do not need to be of the same class... but users may be aware of the type of pages they are queering, moreover when using their own wikiParseFunction.

Parameters baseURL, format and query are not intended for end users.

Value

A list containing the wiki content of the required pages or the formatted objects returned by the wikiParseFunction applied to each page.

See Also

extractTags, getCategoryElements

Examples

res <- getPages(titles = "Rs1234")
res

res <- getPages(titles = c("Rs1234", "Rs1234(A;A)", "Rs1234(A;C)"))
res

myfun <- function(x) substring(x, 1, 5)
lapply(res, myfun)

res <- getPages(titles = c("Rs1234", "Rs1234(A;A)", "Rs1234(A;C)"),
wikiParseFunction = myfun)
res

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