DanteR: Proteomics data analysis tool
Version 0.1.1

Proteomics data analysis tool

Browse man pages Browse package API and functions Browse package files

AuthorTom Taverner
Date of publication2011-05-04 08:03:04
MaintainerTom Taverner <thomas.taverner@pnl.gov>
LicenseGPL (>= 2)
Version0.1.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DanteR", repos="http://R-Forge.R-project.org")

Man pages

ANOVA: Data set ANOVA
DanteR: DanteR
get.dataset.factors: Put factors into a choiceItem
get.dataset.row.metadata.fields: Put row metadata fields into a choiceItem
get.factors: Get row metadata
get.ProtInfo: Get row metadata

Functions

ANOVA Man page Source code
Aggregate Source code
Boxplots Source code
CensorANOVA Source code
CentralTendency Source code
ColorByFactor Source code
Column_Metadata Source code
CorrScatterPlot Source code
Correlation2Dmatrix Source code
CorrelationEllipses Source code
CorrelationHeatmap Source code
CorrelationScatterPlot Source code
CountRollup Source code
Create.Metadata.Table Source code
DataCleaning Source code
DataPlot Source code
DiffExp Source code
DiffExpressed Source code
Filter Source code
FilterMissing Source code
FilterOnANOVA Source code
FilterOnRowIds Source code
Fisher Source code
FoldChanges Source code
GetLinksToMetadata Source code
HeatmapClusters Source code
Histogram Source code
IADJ_pvals Source code
ImputeData Source code
IsCompleteData Source code
KNNWimpute Source code
KNNWsplitImpute Source code
KruskalWalis Source code
LR Source code
Link_To_Metadata Source code
LoadQRollupXLSX Source code
LoessNormalization Source code
LogT Source code
MAD Source code
MADdata Source code
MAplots Source code
MBfilter Source code
MBimpute Source code
MeanCenter.Div Source code
Merge Source code Source code
MergeDataColumns Source code
NewDataFrame Source code
NewQuantileN Source code
NonParametricMethods Source code
OrderByFactor Source code
PAdj Source code
PCAplot Source code
PatternScore Source code
PatternSearch Source code
Plot3D Source code
PlotDataAgainstMean Source code
PlotRows Source code
Plot_All_Links Source code
QQplot Source code
QRollup Source code
QuantileN Source code
RRollup Source code
RRollupPlots Source code
RVersionOK Source code
Row_Metadata Source code
SVDimpute Source code
SaveWithProts Source code
ShapiroWilks Source code
SingleMAplot Source code
Smoosh Source code
SpectralCounting Source code
VennDiagrams Source code
VennDiagrams2 Source code
VennPlot Source code
VolcanoPlot Source code
Wilcoxon Source code
ZRollup Source code
aggregate_on_group Source code
anovaPvals Source code
biplot.dante Source code
checkPackage Source code
cleanmatrix.1 Source code
color2D.matplot.1 Source code
column.metadata.colnames Source code
column.metadata.rownames Source code
copy.metadata Source code
create.aliases Source code
createMSMSdt.SpectralCount.1 Source code
createMSMSdt.old Source code
customScale Source code
dante Man page Source code
dfedit.options Source code
doLOESSreplicates Source code
doLinearRegression Source code
eigen_norm Source code
eigen_norm1 Source code
eigen_norm2 Source code
eigen_pi Source code
enter_pi Source code
factor.values Source code
fillmissing Source code
get.ODBC.table Source code
get.ODBC.table.names Source code
get.ProtInfo Man page Source code
get.column.metadata.key Source code
get.column.metadata.table Source code
get.column.metadata.table.name Source code
get.csv.colnames Source code
get.dataset.column.metadata.fields Source code
get.dataset.factors Man page
get.dataset.row.metadata.fields Man page Source code
get.factors Man page Source code
get.factors.column Source code
get.file.type Source code
get.metadata.fields Source code
get.metadata.obj Source code
get.row.metadata.key Source code
get.row.metadata.table Source code
get.row.metadata.table.name Source code
get.table Source code
get.table.names Source code
get_all_linked_table_names Source code Source code
get_and_assign_obj Source code
get_coefs Source code
get_eigenpep Source code
get_pattern Source code
get_pi Source code
getmatrix Source code
gfile_temp Source code
heatmap.corr Source code
heatmap.dante Source code
identifyPch Source code
imp_elim_proteins Source code
incidence.table.1 Source code
installPackage Source code
installPackages Source code
loadfile Source code
logTransform Source code
make.count.xtab Source code
make.formula.string Source code
merge_all_tables Source code
merge_tables Source code
mmul Source code
my.Psi Source code Source code Source code
my.Psi.dash Source code Source code Source code
my.setwd Source code
names.vector Source code
olBarplot Source code
open.MS.csv Source code
open.expression.wizard Source code
outlier.1 Source code
overLapper Source code
panel.cor Source code
panel.hist Source code
panel.ma Source code
panel.myfitline Source code
panel.plane Source code
phi Source code Source code Source code
plot.eigentrends Source code
plotCurrProt.2 Source code
plotCurrProt.RefRup Source code
plsFactors Source code
protein.Qrollup Source code
protein.Qrollup.1 Source code
protein.rollup Source code
protein.rollup1 Source code
protein.rollup2 Source code
protein_var Source code
protlevel_pvals Source code
pvalsNormal Source code
qqline.1 Source code
qqplot.1 Source code
ragged.cbind Source code
read_in_table Source code
refresh_all_fields Source code
remove.duplicates Source code Source code
remove.emptyProtInfo Source code
remove.outliers Source code
resort_table Source code
rm.outlier.1 Source code
rnorm.trunc Source code Source code Source code
row.metadata.colnames Source code
row.metadata.rownames Source code
save.ODBC.table Source code
save_tables Source code
scale.data Source code
scatter.3D Source code
select_pvals Source code
sendmatrix Source code
set.column.metadata.key Source code
set.column.metadata.table Source code
set.metadata.column.fields Source code
set.metadata.obj Source code
set.metadata.row.fields Source code
set.row.metadata.key Source code
set.row.metadata.table Source code
setpar Source code
splitForAnova Source code
splitmissing Source code
splitmissing.fLevel Source code
splitmissing.factor Source code
stolen_limma_normalizeQuantiles Source code
subsNAvectorColumnWise Source code
subsNAvectorRowWise Source code
sva.id Source code
toggle.dataset.factors Source code
update.aliases Source code
venn.1 Source code
vennPlot Source code
zscores Source code

Files

R
R/aaaStart.r
R/SpectralCounting.R
R/MAD.R
R/QQplot.R
R/PlotXY.R
R/MBFilter.R
R/SVDimpute.R
R/KNNWimpute.R
R/CorrelationHeatmap.R
R/ShapiroWilks.R
R/overLapper.R
R/CensorANOVA.r
R/ImputeData.R
R/NewQuantileN.r
R/Merge.R
R/ANOVA.R
R/VennPlot.R
R/PAdjust.R
R/CorrScatterPlot.r
R/LinearRegression.R
R/PlotDataAgainstMean.r
R/VolcanoPlot.R
R/NewDataFrame.r
R/ReadTable.r
R/MAplots.R
R/gfile_temp.r
R/Histogram.R
R/KruskalWalis.R
R/CentralTendency.r
R/PCAplot.R
R/PlotRows.R
R/MergeDataColumns.R
R/CorrelationScatterPlot.R
R/eigen_norm_addon.R
R/MiscCommands.R
R/RRollupPlots.R
R/NonParametricMethods.R
R/DanteR.r
R/VennDiagrams2.R
R/settings.R
R/Metadata.R
R/ZRollup.R
R/LogTransform.R
R/GetDifferentiallyExpressed.r
R/FilterOnANOVA.R
R/VennDiagrams.R
R/PatternScore.r
R/FilterMissing.R
R/DataCleaning.R
R/Wilcoxon.R
R/QuantileN.R
R/SaveTables.r
R/EigenMS.R
R/OpenQRollupCSV.r
R/zzzDialogs.r
R/RRollup.R
R/HeatmapClusters.r
R/Filter.r
R/ColorByFactor.r
R/FilterOnRowIds.R
R/LoadQRollupXLSX.r
R/CorrelationEllipses.R
R/PeptideCount.R
R/AnovaMethods.R
R/QRollUp.R
R/Correlation2Dmatrix.R
R/Boxplots.R
R/FoldChanges.R
R/MBImpute.r
R/LoessNormalization.R
NAMESPACE
inst
inst/doc
inst/doc/crosslink_icon.png
inst/doc/RRollup.png
inst/doc/Rprofile.site
inst/doc/pattern.png
inst/doc/LogTransform.png
inst/doc/smoosh.png
inst/doc/new-file.png
inst/doc/PCAplot.png
inst/doc/aggregate.PNG
inst/doc/save-file-1.png
inst/doc/fisher.PNG
inst/doc/CorrScatterPlot.PNG
inst/doc/refresh.PNG
inst/doc/ZRollup.png
inst/doc/Histogram.png
inst/doc/ellipse.PNG
inst/doc/QQ.png
inst/doc/merge.png
inst/doc/define-factors.png
inst/doc/venn.png
inst/doc/QRollup.png
inst/doc/nova.PNG
inst/doc/RRollup2.png
inst/doc/summarize.png
inst/doc/bigredx.png
inst/doc/dante.png
inst/doc/volcanoplot1.png
inst/doc/HeatmapClusters.png
inst/doc/Rollup.png
inst/doc/PatternScore.PNG
inst/doc/QQplot.png
inst/doc/alias.png
inst/doc/anova.png
inst/doc/plot_against_row_means.png
inst/doc/CorrelationPlot.png
inst/doc/cogwheel.png
inst/doc/save-file-2.png
inst/doc/alias-off.png
inst/doc/ma.png
inst/doc/open-file.png
inst/doc/scatter3d.PNG
inst/doc/scatter3.PNG
inst/doc/LoessNormalization.png
inst/doc/Boxplots.png
inst/doc/scatter.PNG
inst/doc/filter.PNG
DESCRIPTION
ChangeLog
man
man/DanteR.rd
man/get.dataset.row.metadata.fields.rd
man/get.dataset.factors.Rd
man/ANOVA.rd
man/get.ProtInfo.Rd
man/get.factors.Rd
DanteR documentation built on May 21, 2017, 3:43 a.m.