Streamline Descriptive Analysis of Quantitative Data Matrices

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Documentation for package ‘quantable’ version 0.2.2

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quantable-package Streamline descriptive analysis of quantitative data matrices
altmanbland altman-bland plot
CV compute CV for each row in matrix
CVlog geometric coefficient of variation (CV for log transformed data) Typically used to create and violin plot
dat2Matrix converts sparse representation to dense where row and col can be character vectors
determineCut determine best Accuracy cuttoff
distmy distance among matrix columns with freely choosable distance function
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 t-test
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 applies the scaling to the columns (samples) by default
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 order
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 for exporting i.e. list of foldchanges) uses write.table TODO : validate if not redundant with other write functions
write.vector write vectors as single column table (usefull for exporting i.e. protein id's) uses write.table