RecountGenotyper

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 with:

# 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.

#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.

#test$predicted_genotype<-GetGenotype(model, test$M, test$S)