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ReproducibleResearchTutorial / pubmedR / man / getQueryCounts.Rd

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\name{getQueryCounts}
\alias{getQueryCounts}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
%%  ~~function to do ... ~~
}
\description{
%%  ~~ A concise (1-5 lines) description of what the function does. ~~
}
\usage{
getQueryCounts(genes, terms, baseline = NULL)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{genes}{
%%     ~~Describe \code{genes} here~~
}
  \item{terms}{
%%     ~~Describe \code{terms} here~~
}
  \item{baseline}{
%%     ~~Describe \code{baseline} here~~
}
}
\details{
%%  ~~ If necessary, more details than the description above ~~
}
\value{
%%  ~Describe the value returned
%%  If it is a LIST, use
%%  \item{comp1 }{Description of 'comp1'}
%%  \item{comp2 }{Description of 'comp2'}
%% ...
}
\references{
%% ~put references to the literature/web site here ~
}
\author{
%%  ~~who you are~~
}
\note{
%%  ~~further notes~~
}

%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
%% ~~objects to See Also as \code{\link{help}}, ~~~
}
\examples{
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (genes, terms, baseline = NULL) 
{
    retmat = matrix(rep(0, length(terms) * length(genes)), nc = length(terms))
    colnames(retmat) = terms
    rownames(retmat) = genes
    pb = txtProgressBar(max = length(terms) * length(genes), 
        style = 3)
    i = 0
    for (gene in genes) {
        for (term in terms) {
            i = i + 1
            setTxtProgressBar(pb, i)
            search = sprintf("\%s AND \%s", term, gene)
            if (!is.null(baseline)) {
                search = sprintf("\%s AND \%s", search, baseline)
            }
            doc = pubmedQuery(search)
            if (length(getNodeSet(doc, "//ErrorList")) > 0) {
                retmat[gene, term] = 0
            }
            else {
                retmat[gene, term] = as.integer(xmlValue(getNodeSet(doc, 
                  "/eSearchResult/Count")[[1]]))
            }
        }
        Sys.sleep(0.33)
    }
    return(retmat)
  }
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ ~kwd1 }
\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line