###### MetaData files ####### The metadata for the WGBS tissue samples: WGBS.getHaplo.sampleInfo.txt The metadata for the RRBS tissue/plasma samples: RRBS.getHaplo.sampleInfo.txt ###### AMF and MHL matrices ####### WGBS MHL matrix: WGBS.getHaplo.mhl.mhbs1.0.rmdup_consistent.useSampleID.txt WGBS AMF matrix: WGBS.getHaplo.amf.mhbs1.0.rmdup_consistent.useSampleID.txt RRBS MHL matrix: RRBS_170609.gethaplo.mhl.mhbs1.0.useSampleID.txt RRBS AMF matrix: RRBS_170609.gethaplo.amf.mhbs1.0.useSampleID.txt ###### R Scripts ###### Data pre-processing and imputation: preprocess_data.R Comparing MHL vs AMF metric signal to noise: mhl_vs_amf.R Quantitative tumor load estimation script: tumor_load_estimation.R Tissue of origin prediction: plasma_prediction.R ###### Additional notes ###### R scripts require the following R packages: -ggplot2 -earth -skmeans -ModelMetrics -caret -ROCR -gplot2 (for heatmap) -reshape -compiler -car (caret dependency) -pbkrtest (caret depedency) The published DMRs file: RRBS_MHBs.sorted.DMR.withID.bed ###### Perl and Shell Scripts ###### Generation of mhl matrix (required for tumor_load_estimation.R): hapinfo2mhl.pl Generation of amf matrix (required for tumor_load_estimation.R if using amf): hapinfo2amf.pl Subset haplotype info to MHB regions (required for tumor_load_estimation.R): mergeHaploInfo_bed.pl Code package for generation of simulation data: MakeSimulationFiles.tar.gz ###### Data files for simulation ###### Final simulated haplotype files for normal plasma (required to replicate the results using tumor_load_estimation.R): NCP_simulation.tar.gz Final simulated haplotype files for colon cancer plasma (required to replicate the results using tumor_load_estimation.R): CCT_simulation.tar.gz Final simulated haplotype files for lung cancer plasma (required to replicate the results using tumor_load_estimation.R): LCT_simulation.tar.gz Lung cancer haplotype files list for simulation (required to replicate the results using tumor_load_estimation.R): lct.hapinfo.list20.txt Colon cancer haplotype files list for simulation (required to replicate the results using tumor_load_estimation.R): cct.hapinfo.list20.txt List of normal plasma subset for training: subset_normal_plasma_training ###### Data files for simulation (download separately) ###### Intitial colon cancer tissue fastq file for sampling: FASTQnames/trainingCCT.fq.names.gz Intitial lung cancer tissue fastq file for sampling: FASTQnames/trainingLCT.fq.names.gz Intitial normal plasma fastq file for sampling: FASTQnames/trainingNCP.fq.names.gz Intitial colon cancer tissue alignment file for sampling: BAMfiles/merged.CCT.bam Intitial lung cancer tissue alignment file for sampling: BAMfiles/merged.LCT.bam Intitial normal plasma alignment file for sampling: BAMfiles/merged.50NCP.bam