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... |
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... |
filterSignificant | filters significant values and returns them as list of... |
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 |
image_nan | Copy of... |
imageWithLabels | image plot with labels |
imageWithLabelsNoLayout | image plot with labels |
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 |
my_jackknife | copute jack knive |
mypairs | normal pairs plot with different pch and plus abline |
mypairsSmooth | smoothScatter pairs |
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... |
panel.hist | histogram panel for pairs function (used as default in... |
plotOneSideVolcano | Plot and filter data coming from one sample single sided... |
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... |
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... |
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... |
write.vector | write vectors as single column table (usefull for exporting... |
xxx_replace_xxx | replace patterns (vector) with replacements (vector) in... |
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