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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# ICAMS
<!-- badges: start -->
[](https://cran.r-project.org/package=ICAMS)
<!-- badges: end -->
In-depth Characterization and Analysis of Mutational Signatures ('ICAMS')
## Purpose
Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<https://doi.org/10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <https://doi.org/10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based"
(i.e. representation as mutuations per megabase) mutational spectra or
signatures.
## Installation
### To install the stable version from [CRAN](https://CRAN.R-project.org/package=ICAMS):
*IMPORTANT* Install the
[Bioconductor](https://www.bioconductor.org/) dependencies first:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("BSgenome")
```
This may be slow; please be patient.
Afterwards, install the latest release version of ICAMS with the R command line:
``` r
install.packages("ICAMS")
```
### To install the latest stable version from [GitHub](https://github.com/steverozen/ICAMS):
``` r
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github(repo = "steverozen/ICAMS")
```
### Get the development version
To use new features in the development version,
you can install ICAMS from the master branch on [GitHub](https://github.com/steverozen/ICAMS/tree/master),
which may not be stable:
``` r
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github(repo = "steverozen/ICAMS", ref = "master")
```
## Reference manual
https://github.com/steverozen/ICAMS/blob/v3.0.6-branch/data-raw/ICAMS_3.0.6.pdf
## Frequently asked questions
#### How to do normalization for "counts-based" catalogs of mutational spectra or signatures to account for differing abundances of the source sequence of the mutations?
You can use *exported* function `TransformCatalog` in ICAMS to normalize the
data. Please refer to the documentation and example of `TransformCatalog` for
more details.
## Citing ICAMS
If you use ICAMS in your work, please cite:
> Rozen SG, Jiang NH, Boot A, Liu M, Wu Y, Huang MN, Chang JG (2021). ICAMS:In-depth Characterization and Analysis of Mutational Signatures. R package version 3.0.6, https://CRAN.R-project.org/package=ICAMS.