R Code

The R scripts are all stored on GitHub:
Links to and descriptions of the R scripts used in the analysis may be found in the table below. The column "number" is a rough ordering of the scripts. More detail about the order can be found in the analysis flowchart below — click on the flowchart to see a larger version. A list of input and output files are given for each script.


Showing 14 items
NumberNameDescriptionInputOutput
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NumberNameDescriptionInputOutput
01 data_import.R Imports data sets from GEO database, cleans and saves relevant data  GSE42118_matrix.Rdata, GSE39141_matrix.Rdata, GSE42865_matrix.Rdata, All_3_sets.Rdata, All_3_metasets.Rdata 
02 normalize.R Normalization of 3 separate data files of clean, raw data All_3_metasets.Rdata, Data/All_3_sets.Rdata All_3_sets_normalized.Rdata 
03 exploratory.R Exploratory Analysis All_3_metasets.Rdata, All_3_sets.Rdata  
04 exploratory_postNorm.r Exploratory Analysis after data normalization All_3_sets_normalized.Rdata All_3_sets_normAndFilt.Rdata 
05 aggregate_raw_norm_filter.R Aggregate the beta values of the probes for each CpG island. All_3_metasets.Rdata, All_3_sets.Rdata, All_3_sets_normAndFilt.Rdata,  CPGI2Probe_betaList_raw.Rdata, All_3_sets_normalized.Rdata, CPGI_betaMeanList__raw.Rdata,CPGI_betaMedianList_raw.Rdata 
06 hcluster.R Clustering procedure for pre, post, normalization data and post normalization filtered data All_3_metasets.Rdata, All_3_sets.Rdata, CPGI_betaMeanList_raw.Rdata, CPGI_betaMedianList_raw.Rdata,   
07 aggregate.R Aggregate the beta values of the probes for each CpG island All_3_metasets.Rdata, All_3_sets_normAndFilt.Rdata CPGI2Probe_betaList.Rdata, CPGI2Probe_MList.Rdata, CPGI_betaList.Rdata, CPGI_MList.Rdata 
08 lme_all.R Fit a linear mixed model CPGI2Probe_MList.Rdata lme_ml.tab, lme-geneset.txt 
09 lme_plp.R Fit a linear mixed model CPGI2Probe_MList.Rdata lme_ml_plp.tab, lme-geneset.txt 
10 differential_methylation_figures.R Differential methylation Figures CPGI2Probe_MList.Rdata, lme.t_ml_all.tab, lme.t_ml_plp.tab,   
11 topGO.R Geneset Enrichment Analysis lme.t_ml_all.tab, lme.t_ml_plp.tab allRes_ALL.txt, allRes_APL.txt 
12 cluster_RPMM.R generate the RPMM fit data for the raw and normAndFilt data All_3_sets.Rdata, All_3_sets_normAndFilt.Rdata mmfit_raw.Rdata, mmfit_normFilt.Rdata 
13 plot_cluster_bootstrap.R cluster the raw, normalized, norm&filtered data using pvclust with bootstrapping significance values; plot both clustering result and the p-value vs. standard error  All_3_sets.Rdata, All_3_sets_normalized.Rdata, All_3_sets_normAndFilt.Rdata result_raw.Rdata, result_norm.Rdata, result_normFilt.Rdata 
14 plot_cluster_RPMM.R  plot and layout the results from RPMM clustering  mmfit_raw.Rdata, All_3_sets.Rdata, mmfit_normFilt.Rdata, All_3_sets_normAndFilt.Rdata RPMM_cluster_raw.pdf, RPMM_cluster_normFilt.pdf 
Showing 14 items