---
title: "Analyzing cell-free DNA methylation data with cfTools"
author: 
  - name: Ran Hu
    affiliation:
      - Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles
      - Institute for Quantitative and Computational Biosciences, University of California at Los Angeles
      - Bioinformatics Interdepartmental Graduate Program, University of California at Los Angeles
    email: huran@ucla.edu
  - name: Mary Louisa Stackpole
    affiliation:
      - Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles
  - name: Shuo Li
    affiliation:
      - Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles
  - name: Xianghong Jasmine Zhou
    affiliation:
      - Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles
      - Institute for Quantitative and Computational Biosciences, University of California at Los Angeles
  - name: Wenyuan Li
    affiliation:
      - Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles
package: cfTools
output: 
  BiocStyle::html_document:
    toc: true
    toc_float: true
    theme: flatly
    highlight: pygments
  BiocStyle::pdf_document: default
abstract: >
  Cell-free DNA (cfDNA) in blood has emerged as an ideal surrogate for 
  tumor biopsy. It can be obtained noninvasively, and provides a 
  comprehensive landscape of the heterogeneous genetic and epigenetic 
  alterations in tumors. The `r Biocpkg("cfTools")` package provides 
  methods for cfDNA methylation data analysis to facilitate cfDNA-based 
  cancer studies, including (1) cancer detection: sensitively detect 
  tumor-derived cfDNA to determine whether plasma samples are from cancer 
  patients or normal individuals; (2) tissue deconvolution: infer the 
  tissue composition of plasma samples.
vignette: >
  %\VignetteIndexEntry{cfTools-vignette}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Introduction

Given the methylation sequencing data of a cell-free DNA (cfDNA) sample, 
for each cancer marker or tissue marker, we deconvolve the tumor-derived 
or tissue-specific reads from all reads falling in the marker region. 
Our read-based deconvolution algorithm exploits the pervasiveness of 
DNA methylation for signal enhancement, therefore can sensitively identify 
a trace amount of tumor-specific or tissue-specific cfDNA in plasma. 

Specifically, `r Biocpkg("cfTools")` can deconvolve different sources of 
cfDNA fragments (or reads) in two contexts:

1. Cancer detection [1]: separate cfDNA fragments into tumor-derived 
fragments and background normal fragments (2 classes), and estimate the 
tumor-derived cfDNA fraction $\theta$ ($0\leq \theta < 1$).

2. Tissue deconvolution [2,3]: separate cfDNA fragments from different tissues 
(> 2 classes), and estimate the cfDNA fraction $\theta_t$ 
($0\leq \theta_t < 1$) of different tissue types (including an unknown type) 
$t$ for a plasma cfDNA sample.

These functions can serve as foundations for more advanced cfDNA-based studies, 
including cancer diagnosis and disease monitoring.

# Installation

`r Biocpkg("cfTools")` is an `R` package available via the 
[Bioconductor](http://bioconductor.org) repository for packages. 
You can install the release version by using the following commands 
in your `R` session:

```{r "install", eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("cfTools")
```

Alternatively, you can install the development version from 
[GitHub](https://github.com/) :

```{r 'install_dev', eval = FALSE}
BiocManager::install("jasminezhoulab/cfTools")
```

# Input data preparation

The two main input files for `CancerDetector()` and `cfDeconvolve()` are

* **Input 1**: fragment-level methylation states (methState), 
which are represented by a sequence of binary values (0 represents 
unmethylated CpG and 1 represents methylated CpG on the same fragment);

* **Input 2**: methylation pattern (paired shape parameters of beta 
distributions) of markers. 

`cfSort()` mainly takes **Input 1** as the only input file.

Section 3.1, 3.2, 3.3 provide an example for generating **Input 1**. 
We require users to provide pre-processed paired-end bisulfite sequencing 
reads (i.e., aligned to the reference genome). For each cfDNA sample, 
users need to prepare (1) the standard (sorted) BED file of the aligned 
reads and (2) the methylation information that *bismark* extracts from 
the aligned reads as input data files. Specifically, 

* Section 3.1 `MergePEReads()`
  * Input: a standard (sorted) BED file of paired-end sequencing reads
  * Output: fragment-level information of cfDNA reads
* Section 3.2 `MergeCpGs()`
  * Input: a `CpG_OT*` file and a `CpG_OB*` file generated by 
  *bismark methylation extractor*
  * Output: methylation information of all CpGs on the same fragment
* Section 3.3 `GenerateFragMeth()`
  * Input: the output lists of `MergePEReads()` and `MergeCpGs()`
  * Output: fragment-level information about methylation states
  
Section 3.4 provides an example for generating **Input 2**. Specifically,

* Section 3.4 `GenerateMarkerParam()`
  * Input: a list of methylation levels (e.g., beta values) for markers, 
  a vector of sample types (e.g., tumor or normal, tissue types) corresponding 
  to the rows of the list, a vector of marker names corresponding to the 
  columns of the list
  * Output: a list containing the paired shape parameters of beta 
  distributions for markers

Example input data files are included within the package:

```{r demo}
library(cfTools)
library(utils)
demo.dir <- system.file("data", package="cfTools")
```
 
## Merge paired-end sequencing reads to fragment-level

Function `MergePEReads()` generates fragment-level information for 
paired-end sequencing reads. The main input file is a standard (sorted) 
BED file (e.g. output of *bedtools bamtobed*) of paired-end sequencing 
reads containing columns of chromosome name, chromosome start, 
chromosome end, sequence ID, mapping quality score, and strand. 

```{r}
PEReads <- file.path(demo.dir, "demo.sorted.bed.txt.gz")
head(read.table(PEReads, header=FALSE), 2)
```

The output is a list in BED file format and/or written to an output 
BED file, where each line contains the information of a cfDNA fragment.

```{r}
fragInfo <- MergePEReads(PEReads)
head(fragInfo, 2)
```

## Merge methylation states of CpGs on two strands to fragment-level

Function `MergeCpGs()` generates fragment-level methylation states of CpGs. 
The main inputs of it are two output files of *bismark methylation extractor*, 
which is a program performing methylation calling on bisulfite treated 
sequencing reads. The `CpG_OT*` file contains methylation information for 
CpGs on the original top strand (OT); the `CpG_OB*` file contains methylation 
information for CpGs on the original bottom strand (OB). Both files contain 
columns of sequence ID, methylation state, chromosome name, chromosome start, 
methylation call.

```{r}
CpG_OT <- file.path(demo.dir, "CpG_OT_demo.txt.gz")
CpG_OB <- file.path(demo.dir, "CpG_OB_demo.txt.gz")
head(read.table(CpG_OT, header=FALSE), 2)
head(read.table(CpG_OB, header=FALSE), 2)
```
The output is a list in BED file format and/or written to an output 
BED file, where each line contains methylation states of all CpGs on the 
same fragment. Column *methState* is a sequence of binary values indicating 
the methylation states of all CpGs on the same fragment (0 represents 
unmethylated CpG and 1 represents methylated CpG).

```{r}
methInfo <- MergeCpGs(CpG_OT, CpG_OB)
head(methInfo, 2)
```

## Generate fragment-level information about methylation states

Function `GenerateFragMeth()` combines the output lists of 
`MergePEReads()` and `MergeCpGs()` into one list, 
which contains both the fragment information and the methylation 
states of all CpGs on each fragment. 

```{r}
fragMeth <- GenerateFragMeth(fragInfo, methInfo)
head(fragMeth, 2)
```

## Generate the methylation pattern of markers

Function `GenerateMarkerParam()` calculates paired shape parameters 
of beta distributions for each marker. There are three main inputs 
to this function: (1) a list of methylation levels (e.g., 
beta values), where each row is a sample and each column is a marker; 
(2) a vector of sample types (e.g., tumor or normal, tissue types) 
corresponding to the rows of the list; (3) a vector of marker 
names corresponding to the columns of the list.

```{r}
methLevel <- read.table(file.path(demo.dir, "beta_matrix.txt.gz"), 
                      row.names=1, header = TRUE)
sampleTypes <- read.table(file.path(demo.dir, "sample_type.txt.gz"), 
                        row.names=1, header = TRUE)$sampleType
markerNames <- read.table(file.path(demo.dir, "marker_index.txt.gz"), 
                        row.names=1, header = TRUE)$markerIndex
print(methLevel)
print(sampleTypes)
print(markerNames)
```

The output is a list containing the paired shape parameters of 
beta distributions for markers, which are delimited by `:`. Users can 
save this list into a file with column names, no row names, and 
columns are delimited by TAB for later use.

```{r}
markerParam <- GenerateMarkerParam(methLevel, sampleTypes, markerNames)
print(markerParam)
```

Note that parameter value `NA:NA` or `0:0` may cause errors in the 
following analyses. Remove these values before using this file.

# Fragments intersecting with marker regions

To make the computation more efficient, users may only keep the fragments 
that overlap with the genomic regions of markers. Here, we provide an 
example of using `R` package `r Biocpkg("GenomicRanges")` to perform the 
intersection. 

First, transform the two BED files into GRanges classes.

```{r message=FALSE}
library(GenomicRanges)

# a BED file of fragment-level methylation information
frag_bed <- read.csv(file.path(demo.dir, "demo.fragment_level.meth.bed.txt.gz"), 
                     header=TRUE, sep="\t")
frag_meth.gr <- GRanges(seqnames=frag_bed$chr, 
                     ranges=IRanges(frag_bed$start, frag_bed$end),
                     strand=frag_bed$strand,
                     methState=as.character(frag_bed$methState))

# a BED file of genomic regions of markers
markers_bed <- read.csv(file.path(demo.dir, "markers.bed.txt.gz"), 
                        header=TRUE, sep="\t")
markers.gr <- GRanges(seqnames=markers_bed$chr, 
                      ranges=IRanges(markers_bed$start, markers_bed$end),
                      markerName=markers_bed$markerName)

head(frag_meth.gr, 2)
head(markers.gr, 2)
```

Then, overlap two GRanges classes and get the fragment-level methylation 
states intersecting with the markers.

```{r}
ranges <- subsetByOverlaps(frag_meth.gr, markers.gr, ignore.strand=TRUE)
hits <- findOverlaps(frag_meth.gr, markers.gr,ignore.strand=TRUE)
idx <- subjectHits(hits)

values <- DataFrame(markerName=markers.gr$markerName[idx])
mcols(ranges) <- c(mcols(ranges), values)

marker.methState <- as.data.frame(cbind(ranges$markerName, 
                                        ranges$methState))
colnames(marker.methState) <- c("markerName", "methState")
head(marker.methState, 4)
```

# Cancer detection with `CancerDetector()`

Function `CancerDetector()` separates cfDNA into tumor-derived fragments 
and background normal fragments and estimates the tumor burden. The main 
inputs are two files: (1) the fragment-level methylation states of reads 
(column `methState`) that mapped to the cancer-specific markers; 
(2) paired shape parameters of beta distributions for cancer-specific markers. 
All columns are delimited by TAB, and the first line is the column names. 
In addition, users can tune the parameter `lambda` to adjust the relative 
level of tumor burden.

```{r}
fragMethFile <- file.path(demo.dir, "CancerDetector.reads.txt.gz")
markerParamFile <- file.path(demo.dir, "CancerDetector.markers.txt.gz")
head(read.csv(fragMethFile, sep = "\t", colClasses = "character"), 4)
head(read.csv(markerParamFile, sep = "\t"), 4)
```

The output is the estimated tumor burden $\theta$ and the normal 
cfDNA fraction $1-\theta$.

```{r}
CancerDetector(fragMethFile, markerParamFile, lambda=0.5, id="test")
```

# Tissue deconvolution with `cfDeconvolve()`

Function `cfDeconvolve()` estimates fractions of cfDNA fragments from 
different tissues (> 2 classes). The main two input files are similar 
to function `CancerDetector()`: (1) the fragment-level methylation states 
of reads (column `methState`) that mapped to the tissue-specific markers; 
(2) paired shape parameters of beta distributions for tissue-specific 
markers. All columns are delimited by TAB, and there is a header line of 
the column names.

```{r}
fragMethFile2 <- file.path(demo.dir, "cfDeconvolve.reads.txt.gz")
markerParamFile2 <- file.path(demo.dir, "cfDeconvolve.markers.txt.gz")
head(read.csv(fragMethFile2, header=TRUE, sep="\t", 
              colClasses = "character"), 4)
head(read.csv(markerParamFile2, header=TRUE, sep="\t", 
              colClasses = "character"), 4)
```
Other input parameters are:

- **Number of tissue types**: a positive integer number *k*. Reads will 
be classified into *k* different tissue types.
- **Read-based tissue deconvolution EM algorithm type**: options are 
`em.global.unknown` (default), `em.global.known`, `em.local.unknown`, 
`em.local.known`.
- **Likelihood ratio threshold**: a positive float number. We suggest this 
number is 2 (default). All reads with likelihood ratio < cutoff (default: 
-1.0, meanin no reads filtering is used) will not be used. Likelihood ratio 
is the max(all tissues' likelihoods)/min(all tissues' likelihoods).
- **EM algorithm maximum iteration number**: a positive integer number. 
Default is 100.
- **Sample ID**: the unique sample ID.

For example:
```{r}
numTissues <- 7
emAlgorithmType <- "em.global.unknown"
likelihoodRatioThreshold <- 2
emMaxIterations <- 100
id <- "test"
```

The output is a list containing the cfDNA fractions of different 
tissue types and an unknown class.

```{r, message=TRUE}
tissueFraction <- cfDeconvolve(fragMethFile2, markerParamFile2, numTissues, 
                               emAlgorithmType, likelihoodRatioThreshold, 
                               emMaxIterations, id)
tissueFraction
```

# Tissue deconvolution with `cfSort()`

Function `cfSort()` estimates fractions of cfDNA fragments derived from 29 
major human tissues. It is the first supervised tissue deconvolution 
approach with deep learning models. The main input file is similar to function 
`CancerDetector()` and `cfDeconvolve()`: the fragment-level methylation 
states of reads (column `methState`) that mapped to the tissue-specific 
markers. Additionally, there are a few more columns which can be derived 
from the output of `MergeCpGs()`.

```{r}
fragMethInfo <- file.path(demo.dir, "cfSort.reads.txt.gz")
head(read.csv(fragMethInfo, header=TRUE, sep="\t", 
              colClasses = "character"), 4)
```
Column *methCount* is the number of methylated CpG sites (methState=1) 
on the fragment, and column *unmethCount* is the number of unmethylated 
CpG sites (methState=0) on the fragment.

The output is a list containing the cfDNA fractions of 29 tissue types.

```{r, message=FALSE}
tissueFraction2 <- cfSort(fragMethInfo, id="demo")
tissueFraction2
```

# Reference

[1] Li W, Li Q, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, 
Wong WH, Alber F, Zhou XJ. CancerDetector: ultrasensitive and non-invasive 
cancer detection at the resolution of individual reads using cell-free DNA 
methylation sequencing data. *Nucleic Acids Res*. 2018 Sep 6;46(15):e89. 
doi: 10.1093/nar/gky423. PMID: 29897492; PMCID: PMC6125664.

[2] Del Vecchio G, Li Q, Li W, Thamotharan S, Tosevska A, Morselli M, Sung K, 
Janzen C, Zhou X, Pellegrini M, Devaskar SU. Cell-free DNA methylation and 
transcriptomic signature prediction of pregnancies with adverse outcomes. 
*Epigenetics*. 2021 Jun;16(6):642-661. doi: 10.1080/15592294.2020.1816774. 
PMID: 33045922; PMCID: PMC8143248.

[3] Li S, Zeng W, Ni X, Liu Q, Li W, Stackpole ML, Zhou Y, Gower A, Krysan K, 
Ahuja P, Lu DS, Raman SS, Hsu W, Aberle DR, Magyar CE, French SW, Han SB, 
Garon EB, Agopian VG, Wong WH, Dubinett SM, Zhou XJ. Comprehensive tissue 
deconvolution of cell-free DNA by deep learning for disease diagnosis and 
monitoring. *Proc Natl Acad Sci U S A*. 2023 Jul 11;120(28):e2305236120. 
doi: 10.1073/pnas.2305236120. Epub 2023 Jul 3. PMID: 37399400.

# Session info {-}
```{r sessionInfo, echo=FALSE}
sessionInfo()
```
