pcaGoPromoter-package: Tools for analyzing data from DNA micro arrays.

In pcaGoPromoter: pcaGoPromoter is used to analyze DNA micro array data

Description

Welcome to the pcaGoPromoter package. The purpose of this package is to ease the analyses of data from genome wide gene expression analysis. Multiple platforms can be used (Affymetrix GeneChip, Illumina expression beadchips, qRT-PCR and more). Probe identifiers should be either Affymetrix Probe Set ID, Gene Symbol or Entrez gene ID.

The overall analysis strategy is to conduct principal component analysis followed by the interpretation of the principal component dimensions by functional annotation for biological function and prediction of regulatory transcription factor networks.

You can learn what objects this package supports with the following command:

'ls("package:pcaGoPromoter")'

Each of these objects has their own manual page detailing where relevant data was obtained along with some examples of how to use it.

Author(s)

Morten Hansen [e-mail] and Jorgen Olsen [e-mail]

Maintainer: Morten Hansen [e-mail]

Examples

ls("package:pcaGoPromoter")

Example output

Loading required package: ellipse
Loading required package: Biostrings
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

 [1] "GOtree"                "GOtreeHits"            "GOtreeWithLeaveOut"   
 [4] "getRankedProbeIds"     "getRankedProbeIds.pca" "pca"                  
 [7] "pcaInfoPlot"           "plot.GOtree"           "plot.pca"             
[10] "primo"                 "primoData"             "primoHits"            
[13] "primoWithLeaveOut"     "print.GOtree"          "print.pca"            

pcaGoPromoter documentation built on Oct. 31, 2019, 5:31 a.m.