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These functions make the R library environment.
The Random Forest implementation used in this work was provided by the R library randomForest [65].
Graphical output was generated using the R library ggplot2, version 2.0.0 [2.0.0
As a measurement of importance of the 909 selected probes, variable importance of projection (VIP) values were calculated using the R library plsVarSel.
Multinomial logistic regression was computed by means of the R library vglm.
A modified version of the R library SNPassoc [44] that allows for tri-allelic SNP status was used.
A Gaussian Mixture Model is fit using the Expectation Maximization algorithm as implemented in the R library CNVtools [18].
These data were then analyzed for fold changes and q-values between two different patient cohorts using the "sam" function in the "siggenes" R library [27].
The variance of the random effect was insignificant (<10−6) and fixed effect estimates and SE did not change (R library lme4).
Genes in the co-expression network around each kinase were analyzed for significant enrichments of GO-BP classes by using R library GOSim [80].
A specific R library that uses the 'S4' system of formal classes and methods was used to process and normalize nylon microarray data [67].
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