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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 |