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<!-- 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%"
)
```
# *methylTFR* : Quantification of DNA Methylation Patterns in TFBS
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`methylTFR` is an R-package to analyze DNA methylation signatures in transcription factor binding sites in each individual cells or samples.
## Installation instructions
Get the latest release `methylTFR` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("methylTFR")
```
And the development version from [GitHub](https://github.com/EpigenomeInformatics/methylTFR) with:
```{r 'install_dev', eval = FALSE}
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("EpigenomeInformatics/methylTFR")
```
## Documentation
Full documentation and vignettes are hosted at
[epigenomeinformatics.github.io/methylTFR](https://epigenomeinformatics.github.io/methylTFR/):
- [Get started](https://epigenomeinformatics.github.io/methylTFR/articles/methylTFR.html) — reading data, computing deviations, and footprints.
- [Case study: memory vs. naive T cells](https://epigenomeinformatics.github.io/methylTFR/articles/memTcells.html) — differential TF activity on bundled example data.
## Quick Start
This is a basic example which shows you how to run `methylTFR` :
```{r example, eval = FALSE}
library(GenomicRanges)
library(dplyr)
library(methylTFRAnnotationHg38) # annotation package for hg38
library(methylTFR)
gcfreqs <- getGCfreq(motifSet = "jaspar2020")
gc_dist <- getGenomeGC("hg38")
tf_bindsites <- getTFbindsites(motifSet = "jaspar2020")
sample_dir <- file.path("samples_dir")
sample_ann <- "samples.tsv" # should contain column name bedFile
# deviation score matrix
deviations <- run_methyltfr(sample_ann, # sample annotation file
sample_dir, # where the EPP files are
threads = 8, # number of threads
chunkSize = 10, # number of chunks to process
sampleColName = "bedFile", # column name for EPP file paths in sample_ann
tf_bindsites = tf_bindsites, # TF binding sites
gcfreqs = gcfreqs, # GC frequency
gc_dist = gc_dist, # GC distribution
filetype = "EPP" # file type
)
```
## Citation
Below is the citation output from using `citation('methylTFR')` in R. Please
run this yourself to check for any updates on how to cite __methylTFR__.
```{r 'citation', eval = requireNamespace('methylTFR')}
print(citation("methylTFR"), bibtex = TRUE)
```