README.Rmd

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# RecountGenotyper

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The goal of RecountGenotyper is to predict the genotype information from the RNA-seq data in Recount3. The available data in Recount3 is in form of total bigwig files (.bw) and alternative files (.zst).

## Installation

You can install the development version of RecountGenotyper from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("raziafrooz/RecountGenotyper")
```

## Genotype calling

This package has two functions:

1) GetMandS()

* This function will take the SNP, bigwig, and alternative file path along with sample id and an tempurary folder. 
* In this function, SNPs will be filtered if the total coverage is lower than 4. After the bigwig files and alternative files are loaded, the M and S values are calculated. The prediction accuracy based on the Allele frequency and total coverage will also be calculated.


```{r}
#test<-GetMandS(snps_path, bigWig_path, coverage_cutoff=4,alt_path, sample_id_rep, temp_folder)
```

2) GetGenotype()

* This function will take the prediciton model, M, and S values. M and S values are provided as columns in GetMandS() funciton. 
* This function will output an array of the predicted genotypes. The order will be the same as GetMandS() funciton.

```{r}
#test$predicted_genotype<-GetGenotype(model, test$M, test$S)
```