quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

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Methods which streamline the descriptive analysis of quantitative matrices. Matrix columns are samples while rows are features i.e. proteins, genes.

Author
Witold Wolski <wewolski@gmail.com>
Date of publication
2016-07-20 00:36:01
Maintainer
Witold Wolski <wewolski@gmail.com>
License
GPL-3
Version
0.2.2
URLs

View on CRAN

Man pages

altmanbland
altman-bland plot
CV
compute CV for each row in matrix
CVlog
geometric coefficient of variation (CV for log transformed...
dat2Matrix
converts sparse representation to dense where row and col can...
determineCut
determine best Accuracy cuttoff
distmy
distance among matrix columns with freely choosable distance...
fisherExact
get p-values using fishers exact test for count data
getBlueScale
create blue color scale
getBlueWhiteRed
create blue white red palette
getDiv
create divergent palette
getGreensScale
create green color scale
getRedScale
create red color scale
getTValuesForVolcano
get p-values of t-test values for volcano
getWRValuesForVolcano
get p-values of wilcoxon rank sum test for volcano
imageColorscale
if you need an colorscale to you imagelables use this
imageWithLabels
image plot with labels
imageWithLabelsNoLayout
image plot with labels
makeROCplot
create density plots of cases and controls and ROC plot
mypairs
normal pairs plot with different pch and plus abline
onesamplegreaterT
One sample single sided t-test on matrix
pairsQQ
pairsplot of QQ plots
plotOneSideVolcano
Plot and filter data coming from one sample single sided...
pvalCorMat
pvalues for correlation matrix -
quantable
Streamline descriptive analysis of quantitative data matrices
removeNArows
Removes rows with more than thresh NA's from matrix
robustscale
robust scaling uses median an mad instead of mean and row...
runFun
running function (default median absolute deviation)
runrobscale
running robust scaling of arefw
runTICscale
running total ion count scaling (TIC)
scaleByGroup
scale data given group
simpleheatmap
heatmap2 facade
split2table
splits names and creates a matrix
sumtop
sums top rows of matrix uses median of row to determine row...
unpivot
unpivot data matrix
uppertriang
get values of upper triangle from matrix
volcanoplot
volcano plot
write.tab
write table in tab delimited no quotes no row.names (usefull...
write.vector
write vectors as single column table (usefull for exporting...

Files in this package

quantable
quantable/NAMESPACE
quantable/R
quantable/R/unpivot.R
quantable/R/OneSampleSingleSidedVolcano.R
quantable/R/scaleByGroup.R
quantable/R/getValuesForVolcano.R
quantable/R/uppertriang.R
quantable/R/write.vector.R
quantable/R/sumtop.R
quantable/R/volcanoplot.R
quantable/R/datadescription.R
quantable/R/removeNArows.R
quantable/R/CV.R
quantable/R/pvalCorMat.R
quantable/R/runFun.R
quantable/R/imageWithLabels.R
quantable/R/distmy.R
quantable/R/altmanbland.R
quantable/R/roc.R
quantable/R/runrobscale.R
quantable/R/dat2Matrix.R
quantable/R/pairsQQ.R
quantable/R/simpleheatmap.R
quantable/R/scales.R
quantable/R/split2table.R
quantable/R/robustscale.R
quantable/R/mypairs.R
quantable/MD5
quantable/DESCRIPTION
quantable/man
quantable/man/mypairs.Rd
quantable/man/imageColorscale.Rd
quantable/man/pairsQQ.Rd
quantable/man/distmy.Rd
quantable/man/pvalCorMat.Rd
quantable/man/runFun.Rd
quantable/man/getTValuesForVolcano.Rd
quantable/man/scaleByGroup.Rd
quantable/man/CV.Rd
quantable/man/write.tab.Rd
quantable/man/write.vector.Rd
quantable/man/determineCut.Rd
quantable/man/unpivot.Rd
quantable/man/volcanoplot.Rd
quantable/man/dat2Matrix.Rd
quantable/man/makeROCplot.Rd
quantable/man/plotOneSideVolcano.Rd
quantable/man/altmanbland.Rd
quantable/man/getWRValuesForVolcano.Rd
quantable/man/sumtop.Rd
quantable/man/getBlueWhiteRed.Rd
quantable/man/fisherExact.Rd
quantable/man/getBlueScale.Rd
quantable/man/removeNArows.Rd
quantable/man/onesamplegreaterT.Rd
quantable/man/imageWithLabels.Rd
quantable/man/quantable.Rd
quantable/man/robustscale.Rd
quantable/man/runTICscale.Rd
quantable/man/getRedScale.Rd
quantable/man/split2table.Rd
quantable/man/uppertriang.Rd
quantable/man/runrobscale.Rd
quantable/man/simpleheatmap.Rd
quantable/man/getGreensScale.Rd
quantable/man/getDiv.Rd
quantable/man/CVlog.Rd
quantable/man/imageWithLabelsNoLayout.Rd