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Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Introduction

Bedgraph files generated by BS pipelines often come in various flavors. Critical downstream step requires aggregation of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Package overview and usage functions

Summary:

• Faster summarization of generic bedGraph files with data.table back-end
• Fills missing CpGs from reference genome
• Vectorized code (faster, memory expensive) and non-vectorized code (slower, minimal memory)
• Built upon SummarizedExperiment with custom methods for CpG extraction, sub-setting, and filtering
• Easy conversion to bsseq object for downstream analysis
• Extensive one click interactive html report generation
• Supports serialized arrays with HDF5Array and saveHDF5SummarizedExperiment

Updates:

see here

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CompEpigen/methrix")

Usage:

Step-1: Extract all CpG loci from the reference genome

> hg19_cpgs = methrix::extract_CPGs(ref_genome = "BSgenome.Hsapiens.UCSC.hg19")
# Extracting CpGs..
# Here is a Chuck Norris joke while you wait..
# Chuck Norris doesn't chew gum. Chuck Norris chews tin foil.
# Done.
# Extracted 28787054 from 86 contigs.

Step-2: Read in bedgraphs and generate a methrix object

Test data is 3 stranded WGBS bedgraphs from MethylcTools

#Example bedgraph files
> bdg_files = list.files(path = system.file('extdata', package = 'methrix'), pattern = "*bdg\\.gz$", full.names = TRUE)

> meth = methrix::read_bedgraphs(files = bdg_files, ref_cpgs = hg19_cpgs, chr_idx = 1, start_idx = 2, M_idx = 3, U_idx = 4,
  stranded = TRUE, collapse_strands = TRUE)
----------------------------
-Preset:        Custom 
--Missing beta and coverage info. Estimating them from M and U values
-CpGs raw:      28,700,086
-CpGs filtered: 28,217,448
-CpGs stranded: 56,434,896
----------------------------
-Batch:         1/1 
-Processing:    C1.bdg.gz
--CpGs missing: 56,434,254
-Processing:    C2.bdg.gz
--CpGs missing: 56,434,231
-Processing:    N1.bdg.gz
--CpGs missing: 56,434,233
-Processing:    N2.bdg.gz
--CpGs missing: 56,434,233
-Finished in:   00:01:19 elapsed (00:01:52 cpu) 

> meth
An object of class methrix
   n_CpGs: 28,217,448
n_samples: 4
    is_h5: FALSE
Reference: Genome Reference Consortium GRCh37

Methrix operations

What can be done on methrix object? Following are the key functions

subset_methrix()    #Subset methrix object based on given condition
write_bedgraphs()   #Writes bedGraphs from methrix object
order_by_sd()       #order methrix object by SD
methrix_report()    #Create a detailed interative html summary report from methrix object
methrix2bsseq()     #Convert methrix to bsseq object
region_filter()	    #Filter matrices by region
remove_uncovered()	#Remove loci that are uncovered across all samples
coverage_filter()   #Filters methrix object based on coverage
methrix_pca()	      #Principal Component Analysis
subset_methrix	    #Subsets 'methrix' object based on given conditions.
get_stats()	        #Estimate descriptive statistics of the object
methrix_report()	  #Creates a detailed interative html summary report from Methrix object

plus other plotting functions..

Speed benchmark

To be added

To do

• Write methods
• Add vignette
• Add examples
• Clear BiocCheck warnings and notes
• Submit to BioConductor for Fall (3.10) release

Note

This repository is under active development