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| quantable-package | Streamline descriptive analysis of quantitative data matrices |
| addSpecialProteins | add special labels |
| altmanbland | altman-bland plot |
| colNAs | get NR of NA's per matrix or data.frame column |
| 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 |
| filterSignificant | filters significant values and returns them as list of data.frames |
| 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 |
| image_nan | Copy of http://stackoverflow.com/questions/20977477/how-to-assign-a-specific-color-to-na-in-an-image-plot |
| jackknifeMatrix | Compute correlation matrix with jack |
| makeROCplot | create density plots of cases and controls and ROC plot |
| matrix_to_tibble | Matrix to tibble (taken from tidyquant) |
| multigroupFCDATA | example data from multigroup analysis |
| multigroupVolcano | plot volcano given multiple conditions |
| mypairs | normal pairs plot with different pch and plus abline |
| mypairsSmooth | smoothScatter pairs |
| my_jackknife | copute jack knive |
| onesamplegreaterT | One sample single sided t-test on matrix |
| pairsQQ | pairsplot of QQ plots |
| panel.cor | correlation panel for pairs plot function (used as default in mypairsSmooth) |
| panel.hist | histogram panel for pairs function (used as default in mypairsSmooth) |
| plotOneSideVolcano | Plot and filter data coming from one sample single sided t-test |
| ProgenesisBuildAnnotation | build annotation from column names |
| ProgenesisRead | reads file exportet from progenesis ProgenesisRead |
| pvalCorMat | pvalues for correlation matrix - |
| quantable | Streamline descriptive analysis of quantitative data matrices |
| removeDecorrelated | remove decorrelated rows |
| 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 |
| rowNAs | get NR of NA's per matrix or data.frame 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 |
| setdiff_data.frame | setdiff for data frames |
| 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 |
| volcano2G | DEPRECATED Volcano plot using ggplot and ggrepel |
| volcano2GB | Volcano with more control |
| 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 |
| xxx_replace_xxx | replace patterns (vector) with replacements (vector) in string or string vector. uses gsub and perl=TRUE taken from <URL: https://stackoverflow.com/questions/26676045> |