annotationTable: Function to Create an annotationTable

In a4Reporting: Automated Affymetrix Array Analysis Reporting Package

Description

This function takes data to be displayed as well as data containing hyperlinks corresponding to displayed data and constructs an object of class annotationTable

Usage

annotationTable(displayData, displayCols = NULL, hrefData = NULL)

Arguments

displayData	data frame containing data that is meant to be displayed in a LaTeX table
displayCols	list of named character vectors (of length one) that function as key-value pairs; the names (keys) correspond to columns for which the hyperlinks should be generated whereas the strings (values) indicate what kind of link should be produced based on the corresponding column in the displayData. The values should be one of "EntrezId" or "GOId".
hrefData	data frame containing hyperlink information for the columns of the same name in the displayData data frame

Details

If hrefData is given, the displayCols are not taken into account. If no hrefData is given, the information in displayCols allows to automatically create the hrefData.

Value

object of class 'annotationTable'

Author(s)

Tobias Verbeke

Examples

  ## some dummy data
  dData <- data.frame(someSymbol = LETTERS[1:5], 
                      accessionNumber = 
                        c("X83928", "V00540", "U21090", "L38487", "M34057"))

  at <- annotationTable(displayData = dData, 
                        displayCols = list(accessionNumber = "EntrezId"))

Example output

Loading required package: annaffy
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

a4Reporting documentation built on May 2, 2019, 4:54 p.m.