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https://github.com/tushiqi/manorm2

MAnorm2 for Normalizing and Comparing ChIP-seq Samples
https://github.com/tushiqi/manorm2

chip-seq differential-analysis empirical-bayes r-package winsorize-values

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MAnorm2 for Normalizing and Comparing ChIP-seq Samples

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README 

          
---

Title: MAnorm2 1.2.2

Author: Shiqi Tu

Date: 2022-10-28

Contact: tushiqi@picb.ac.cn

---



# Introduction



MAnorm2 is designed for normalizing and comparing

[ChIP-seq](https://en.wikipedia.org/wiki/ChIP-sequencing) signals across

individual samples or groups of samples. The latest version of MAnorm2 is

always available in the [CRAN](https://cran.r-project.org) repository and

can thus be easily installed by typing `install.packages("MAnorm2")` in an

R session.



For older versions of MAnorm2, select a package from under the `dist` folder,

download it, and type `install.packages("/path/to/the/package", repos = NULL)`.

In this way, you may need to pre-install some dependencies of MAnorm2. The

current dependencies of the latest MAnorm2 version include locfit (>= 1.5.9),

scales (>= 0.3.0), and statmod (>= 1.4.34). All these packages are available in

the [CRAN](https://cran.r-project.org) repository. For dependencies of other

MAnorm2 versions, refer to the `Imports` field in the corresponding

`DESCRIPTION` file.



Sections below give a brief description

of the application scope of MAnorm2 as well as its capability. For a full

documentation of MAnorm2, download the HTML version of its vignette from

[here](https://github.com/tushiqi/MAnorm2/tree/master/utility/vignette-MAnorm2)

and use a browser to open it, or type the following code in an R session

after installing MAnorm2:



```r

browseVignettes("MAnorm2")

```



# Format of Input Data



For employing the machinery implemented in MAnorm2, you need to prepare a

table that profiles the ChIP-seq signal in each of a list of genomic intervals

for each of a set of ChIP-seq samples. The following table provides such an

instance:



| chrom|  start|    end| s1.read\_cnt| s2.read\_cnt| s1.occupancy| s2.occupancy|

|-----:|------:|------:|------------:|------------:|------------:|------------:|

|  chr1|  28112|  29788|          115|            4|            1|            0|

|  chr1| 164156| 166417|          233|          194|            1|            1|

|  chr1| 166417| 168417|          465|          577|            1|            1|

|  chr1| 168417| 169906|           15|           34|            0|            1|



(See the `H3K27Ac` dataset bundled with MAnorm2 for another example, and type

`library(MAnorm2); ?H3K27Ac` in an R session for a detailed description of it.)



To be specific, each row of the table represents a genomic interval; each of

the `read_cnt` variables corresponds to a ChIP-seq sample and gives the numbers

of reads from the sample that fall within the genomic intervals (i.e., the raw

read counts); the `occupancy` variables correspond to the `read_cnt`

variables one by one and specify the occupancy status of each genomic interval

in each sample. Note that an occupancy status of 1 indicates the interval

is enriched with reads in the sample (compared with, for example,

the surrounding genomic regions or the corresponding input sample). In

practice, the occupancy status of a genomic interval in a certain ChIP-seq

sample could be determined by its overlap with the

[peaks](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137)

of the sample. Note also that MAnorm2 refers to an interval as occupied by a

sample if the interval is enriched with reads in the sample.



[MAnorm2_utils](https://github.com/tushiqi/MAnorm2_utils) is specifically

designed to coordinate with MAnorm2, and we strongly recommend using it to

create input tables of MAnorm2.



# Application Scope



Although MAnorm2 has been designed to process ChIP-seq data, it could be

applied in principle to the analysis of any type of data with a similar

structure, including

[DNase-seq](https://en.wikipedia.org/wiki/DNase-Seq),

[ATAC-seq](https://en.wikipedia.org/wiki/ATAC-seq) and

[RNA-seq](https://en.wikipedia.org/wiki/RNA-Seq) data.

The only problem associated with such extensions is how to naturally define

"peaks" for specific data types.



Most of the peak callers originally devised for ChIP-seq data

(e.g., [MACS 1.4](https://pypi.org/project/MACS/)) also

work for DNase-seq and ATAC-seq data. For RNA-seq data, each row of the input

table should stand for a gene, and we recommend setting a cutoff (e.g., 20) of

*raw read count* to define "peak" genes.



# Continuous Distribution



In spite of the discrete nature of read counts, MAnorm2 uses continuous

distribution to model ChIP-seq data by first transforming raw read counts into

raw signal intensities. By default, MAnorm2 completes the transformation by

simply adding an offset count to each raw count and taking a base-2 logarithm.

Practical ChIP-seq data sets, however, may be associated with various

confounding factors, including batch effects, local sequence compositions and

background signals measured by input samples. On this account, functions in

MAnorm2 have been designed to be independent of the specific transformation

employed. And any methods for correcting for confounding factors could be

applied before invoking MAnorm2, as long as the resulting signal intensities

could be approximately modeled as following the normal distribution (in

particular, consider carefully whether it is necessary to apply a logarithmic

transformation in the final step).



The primary reason for which MAnorm2 models ChIP-seq signals as

continuous random variables is that the mathematical theory of count

distributions is far less tractable than that of the normal distribution.

For example, current statistical methods based on the negative binomial

distribution are frequently relied on approximations of various kinds.

Specifically, variance (or dispersion) estimates for individual genomic

intervals are typically treated as known parameters, and their uncertainty

can hardly be incorporated into the statistical tests for identifying

differential signals.



Besides, after an extensive correction for confounding factors,

the resulting data range is almost certainly not limited to non-negative

integers, and the data may have lost their discrete nature and be more akin

to a continuous distribution. Moreover, transforming read counts towards the

normal distribution unlocks the application of a large repository of mature

statistical methods that are initially developed for analyzing continuous

measurements (e.g., intensity data from microarray experiments). Refer to the

[voom](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-2-r29)

article for a detailed discussion of this topic.



# Normalization



MAnorm2 implements a robust method for normalizing raw signal intensities

across any number of ChIP-seq samples.



Technically, it considers the common peak regions of two ChIP-seq samples

(i.e., the genomic intervals occupied by both samples; see also the section of

[Format of Input Data](#format-of-input-data)) to have globally invariant

signals between them. Based on this assumption, MAnorm2 applies a linear

transformation to the raw signal intensities of one of the two samples such

that



 1. the resulting M values (differences in signal intensities between the two

    samples) at the common peak regions have an arithmetic mean of 0;

 2. [sample Pearson correlation coefficient](https://en.wikipedia.org/wiki/Pearson_correlation_coefficient#For_a_sample)

    between the resulting M and A values at the common peak regions is 0 (A

    values refer to average signal intensities across the two samples).



This procedure is for normalizing a pair of ChIP-seq samples. It can be

extended to normalization of any number of samples so that the normalized

signal intensities are comparable across all of them. For more information

regarding the normalization method implemented in MAnorm2, type the

following code in an R session after installing it:



```r

library(MAnorm2)

?normalize

?normBioCond

```



# Differential and Hypervariable Analyses



MAnorm2 designs a self-contained system of utility functions for calling

differential ChIP-seq signals between two or more biological conditions, 

each with or without replicate samples. It also implements a method named

HyperChIP for calling hypervariable ChIP-seq signals across samples. To be

noted, the framework implemented in MAnorm2 for differential and hypervariable

analyses requires the input signal intensities to have been normalized but 

is independent of the specific normalization method. 

This means that any normalization and/or bias

correction tools could be adapted to 

MAnorm2, as long as the resulting signal measurements are suited to be

modeled by normal distribution. For example, for highly regular samples,

you might want to perform the normalization based on their *size factors*

(refer to the `normalizeBySizeFactors` function in MAnorm2 for details).



Technically, MAnorm2 has implemented an S3 class named "bioCond" for

grouping ChIP-seq samples belonging to the same biological condition,

and it has devised a number of functions for handling objects of this

class. Taking advantage of these functions, you can



 1. call genomic intervals with differential ChIP-seq signals between

    two or more bioConds;

 2. call genomic intervals with hypervariable ChIP-seq signals across multiple

    samples or bioConds;

 3. perform hierarchical clustering on a set of ChIP-seq samples or bioConds by

    measuring the distance (i.e., dissimilarity) between each pair of them.



Note that, for the samples grouped into a bioCond, MAnorm2 models the

relationship between observed mean signal intensities at individual intervals

and the associated (observed) variances. In practice, this modeling strategy

could compensate for the lack of sufficient replicates for deriving accurate

variance estimates for individual intervals. And each of the above

analyses takes advantage of the modeling of mean-variance trend to improve

variance estimation.



For an overview of the interface functions provided by MAnorm2, type the

following code in an R session after installing it:



```r

library(MAnorm2)

?MAnorm2

```



# Citation



To cite the MAnorm2 package in publications, please use



> Tu, S., et al.,

> *MAnorm2 for quantitatively comparing groups of ChIP-seq samples*.

> Genome Res, 2021. **31**(1): p. 131-145.



If you have performed MA normalization with a pseudo-reference profile as

baseline, or have employed a Winsorization-based robust parameter estimation

framework, or have performed a hypervariable analysis,

please cite additionally



> Chen, H., et al.,

> *HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples*.

> Genome Biol, 2022. **23**(1): p. 62.