A set of scripts and auxiliary functions to perform aJIVE and iPCA on different omic layers.
Main R scripts:
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datafiltering.R : filters the omic data. mRNA is filtered based on variance (5000), CpGs are selected from the same genes as mRNA, missing values >40% eliminated, extreme M values (>3) eliminated miRNA all included needs filtering.R
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aJIVE.R: runs ajive on the filtered data. ranks chosen by profile likelihood needs ajive.dataprep.R, show.var.explained.ajive and aJIVE package screeplots also plotted (needs Screeplots.R)
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predictions.R: in-sample, CV and random forests for predictions of case vs control and metastasis on the aJIVE results