quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

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

AuthorWitold Wolski <wewolski@gmail.com>
Date of publication2016-07-20 00:36:01
MaintainerWitold Wolski <wewolski@gmail.com>
LicenseGPL-3
Version0.2.2
https://github.com/protViz/quantable

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

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