oneChannelGUI: Starting oneChannelGUI package

In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

Description

Starting oneChannelGUI package. oneChannelGUI contains a set of functions extending the capabilities of affylmGUI package

Usage

goseqInterface()
DESeqInterface()
EDAwithinLane()
EDAbetweenLane()
EDAboxplot()
EDAbiasPlot()
AboutextendedaffylmGUI()
AboutaffylmGUI()
oneChannelGUI()
oneChannelGUIHelp()
maSigProHelp()
siggenesHelp()
oneChannelGUIHelp()
initialize.extAffylmGUI()
OpenExonandTargetsfiles()
GOstatsHelp()
SaveLimmaFile()
NewLimmaFile()
NewLimmaFileNGS()
OpenLimmaFile()
OpenALimmaFile(FileName)
OpenAFile(FileName)
OpenExonFile()
OpenLargeFile()
changeMenu()
oneChannelGUI.start()
libraryFilesDir()
whichKindOfArray()
intronicBg()
ExportNormalizedExpressionValues1()
ExportNormalizedExpressionValues()
ExportfeatureNames()
SaveAsLimmaFile()
addAnnLib()
OpenCDFandTargetsfiles()
ComputeLinearModelFit()
GetNormalizationMethod()
NormalizeNow()
ComputeContrasts()
midasFilter()
dabgFilter()
largedatasetNorm()
RankProdHelp()
affyPLMHelp()
genefilterHelp()
pamrHelp()
pdmclassHelp()
sizepowerHelp()
ssizeHelp()
OpenAGeoFile(FileName)
OpenGeoFile()
OpenGeoFiles()
OpenNgsfiles()
recoverUnfiltered()
delete.ML()
affyPlotMA()
changes()
aptFolder()
javaFolder()
deleteLocalData()
SetED()
chooseEDir()
.annotation(eset)
.myfindOverlaps(x,y)
log2Conversion()
.myrk(x,df)
exportFASTA()
OpenmiRanalyserfiles()
OpenmiRProfiles()
OpenmiRExpress()
OpenmiRShrimp()
OpenmiRBam()
ngsperlDownload()
meVDownload()
extPckInfo()
startmeV()
tuxedoMenu()
setBinDir()
fastQC()
openPdf()
closePdf()
plotDE.exons()
topTable.genes()
importfusions()
fusionNS()
fusionfilter()
chimeraseq()
tophatrun()
addga()
fusionpeptides()
plotcoverage()
desCounts()
miRNAde()
downloadShrimp()
wrapperMirnaCounts(working.dir, out.dir, org = "hsa", threads = 1, cutadapt.path = "/usr/local/bin/cutadapt", parallel = FALSE, ...)
deseq2Processing()
enrich(group, permutations = permutations)
loadmirnapath(mirnafile = "mirna_input.txt", mirnacol = "miRNA.id",
                 assayidcol = "ASSAYID", groupcol = "GROUP",
                 filterflagcol = "FILTERFLAG", expressioncol = NA,
                 foldchangecol = NA, pvaluecol = NA)
mirPath()
mirnaTable(mirnaobj, groups = NULL, format = "Tall", Significance
                 = 0.2, na.char = NA, pvalueTypes = c("pvalues",
                 "permpvalues"), maxStringLength = NA, pathwaysNames =
                 hs.path.name)
permuting(perm)
runEnrichment(Composite = TRUE, groups = NULL, permutations = 0)

Arguments

FileName	Internal argument not to be set by the user
eset	Internal argument not to be set by the user
x	Internal argument not to be set by the user
y	Internal argument not to be set by the user
df	Internal argument not to be set by the user
group	Internal argument not to be set by the user
working.dir	Internal argument not to be set by the user
out.dir	Internal argument not to be set by the user
org	Internal argument not to be set by the user
threads	Internal argument not to be set by the user
cutadapt.path	Internal argument not to be set by the user
parallel	Internal argument not to be set by the user
mirnafile	Internal argument not to be set by the user
mirnacol	Internal argument not to be set by the user
assayidcol	Internal argument not to be set by the user
groupcol	Internal argument not to be set by the user
filterflagcol	Internal argument not to be set by the user
foldchangecol	Internal argument not to be set by the user
pvaluecol	Internal argument not to be set by the user
mirnaobj	Internal argument not to be set by the user
groups	Internal argument not to be set by the user
format	Internal argument not to be set by the user
Significance	Internal argument not to be set by the user
na.char	Internal argument not to be set by the user
pvalueTypes	Internal argument not to be set by the user
maxStringLength	Internal argument not to be set by the user
pathwaysNames	Internal argument not to be set by the user
Composite	Internal argument not to be set by the user
permutations	Internal argument not to be set by the user
...	Internal argument not to be set by the user
perm	Internal argument not to be set by the user
expressioncol	Internal argument not to be set by the user

Details

This function launches a modify version of the Graphical User Interface by James Wettenhall for the limma package by Gordon Smyth. The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide a simple interface to various tools for quality control and statistical analysis of Affymetrix gene chips.

Author(s)

Raffaele A Calogero

Examples

#  library(oneChannelGUI)
## To start the affylmGUI with the modifications
#oneChannelGUI()

oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.