xtable-methods: Methods for Function xtable in Package 'annotationTable'

In a4Reporting: Automated Affymetrix Array Analysis Reporting Package

Description

xtable methods for several a4 objects, such as annotationTable objects, topTable objects etc.

Methods

x = "annotationTable", caption = "missing", label = "missing", align = "missing", digits = "missing", display = "missing"

generates a LaTeX representation for the given annotationTable

x = "annotationTable", caption = "ANY", label = "ANY", align = "ANY", digits = "ANY", display = "ANY"

generates a LaTeX representation for the given annotationTable

x = "annotationTable", caption = "ANY", label = "ANY", align = "ANY", digits = "numeric", display = "ANY"

generates a LaTeX representation for the given annotationTable

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"))
  xat <- xtable(at)
  print(xat, include.rownames = FALSE)

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, cbind, colMeans, colSums, colnames, 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

% latex table generated in R 3.4.1 by xtable 1.8-2 package
% Fri Mar  9 08:56:15 2018
\begin{table}[ht]
\centering
\begin{tabular}{ll}
  \hline
someSymbol & accessionNumber \\ 
  \hline
A & \href{http://www.ncbi.nlm.nih.gov/gene/X83928}{X83928} \\ 
  B & \href{http://www.ncbi.nlm.nih.gov/gene/V00540}{V00540} \\ 
  C & \href{http://www.ncbi.nlm.nih.gov/gene/U21090}{U21090} \\ 
  D & \href{http://www.ncbi.nlm.nih.gov/gene/L38487}{L38487} \\ 
  E & \href{http://www.ncbi.nlm.nih.gov/gene/M34057}{M34057} \\ 
   \hline
\end{tabular}
\end{table}

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