Re-analysis Final Code and Data
R code for reproducing Figure 2
-ggplot2
-earth
-skmeans
-ModelMetrics
-caret
-ROCR
-gplot2 (for heatmap)
-reshape
-compiler
Instructions: Please have the perl scripts in the working directory when running tumor_load_estimation.R. The shell and perl code package for making simulation file are provided to perform random sampling of sequencing reads and require both a list of fastq names (to be sampled) and a mapped BAM files (to pull the sampled reads from).
Instructions: These files provide descriptions of the samples.
Instructions: These files are input data for R code above. AMF (average weighted methylation frequency) matrices are provided to perform analysis of AMF versus MHL.
Instructions: After downloading, use tar utility to uncompress all three data folders and have all the files in the working directory when running tumor_load_estimation.R
Methylation_Haplotype_Analysis_v1.2.tar.gz
No installation of this package is required.
analyzeMethylation - quantify methylation levels from haplotype files with one of AMF, IMF, and MHL.
USAGE: analyzeMethylation.sh [list of haplotype files] [region file] <MHL|AMF|IMF>
MethylationHaplotypeGenerator_V1 - generate
methylation haplotype files using version 1 code. Note that this version
only works for data that have been aligned to hg19.
USAGE: MethylationHaplotypeGenerator_V1.sh <RRBS|WGBS> [target bed file] [cpg position file] [bam file] [output name prefix]
MethylationHaplotypeGenerator_V2 - generate methylation haplotype files using version 2 code. This software is best used with BAM files generated from the BisReadMapper
pipeline. Please make sure your BAM files contain flags for Crick reads
in the reverse complementary orientation and that paired-end reads are
matched by identical read IDs. Quality scores must be in PHRED 33 base.
USAGE: MethylationHaplotypeGenerator_V2.sh [cpg position file] [bam file] [output file prefix name]
make_mappable_bins - generate mappable regions file from BAM
USAGE: ./scripts/make_mappable_bins.sh [merged bam file] [minimum mapping depth]
getMHBs - generate methylation haplotype blocks
using version 1 code. Make mappable bins first using the
make_mappable_bins.sh shell script. Next, methylation haplotype block
calling must be performed with MethylationHaplotypeGenerator scripts V1
or V2. V2 script can call a significantly greater number of haplotypes.
In Guo et. al. 2017, we set a highly stringent PHRED score cut off using
V1 which resulted in fewer methylation haplotypes. See information for
methylation haplotype generator softwares. Version 1 of
MethylationHaplotypeGenerator will require the mappable bin file above
to be used as the target file. Methylation haplotype block
identification can be performed with haplotype files generated from V1
or V2. Haploinfo file for chr22 from the 61 WGBS in Guo et. al. 2017 is
provided to reproduce the MHBs for chr22.
USAGE: getMHBs.sh [haplotype file] [target bed] [minimum LD R2 cutoff] [output name prefix]