Streamline Descriptive Analysis of Quantitative Data Matrices

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Documentation for package ‘quantable’ version 0.3.6

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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 <https://stackoverflow.com/questions/26676045>