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.

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AuthorWitold Wolski <wewolski@gmail.com>
Date of publication2016-07-20 00:36:01
MaintainerWitold Wolski <wewolski@gmail.com>

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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...


altmanbland Man page
CV Man page
CVlog Man page
dat2Matrix Man page
determineCut Man page
distmy Man page
fisherExact Man page
getBlueScale Man page
getBlueWhiteRed Man page
getDiv Man page
getGreensScale Man page
getRedScale Man page
getTValuesForVolcano Man page
getWRValuesForVolcano Man page
imageColorscale Man page
imageWithLabels Man page
imageWithLabelsNoLayout Man page
makeROCplot Man page
mypairs Man page
onesamplegreaterT Man page
pairsQQ Man page
plotOneSideVolcano Man page
pvalCorMat Man page
quantable Man page
quantable-package Man page
removeNArows Man page
robustscale Man page
runFun Man page
runrobscale Man page
runTICscale Man page
scaleByGroup Man page
simpleheatmap Man page
split2table Man page
sumtop Man page
unpivot Man page
uppertriang Man page
volcanoplot Man page
write.tab Man page
write.vector Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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