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Getting Started with tso500R

Source: vignettes/getting-started.Rmd
getting-started.Rmd

Introduction

Welcome to tso500R! This guide will help you get started with analyzing TSO500 data.

Installation 

pak::pak("Boehringer-Ingelheim/TSO500R")

Basic Workflow

1. Load Data 

library(tso500R)

# Quality metrics
qc_data <- read_qmo_data("/path/to/output/")

# Variant data
variant_data <- read_cvo_data("/path/to/output/")

2. Extract Variants 

small_variants <- read_small_variants(variant_data)
fusions <- read_fusions(variant_data)
cnvs <- read_gene_amplifications(variant_data)

3. Filter and Process 

filtered_variants <- small_variants |>
  process_and_filter_small_variant_data()

4. Visualize 

plot_af_per_variant_consequence(filtered_variants)
plot_af_histogram_per_sample(filtered_variants)

Next Steps