# ReproducibleResearchTutorial / pubmedR / man / getQueryCounts.Rd

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 \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