---
title: "Getting Started with molpathR"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Getting Started with molpathR}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
resource_files:
- figures/logo.svg
- figures/logo-dark.svg
---
[](https://github.com/CTTIR/molpathR/actions/workflows/R-CMD-check.yaml)
[](https://cttir.github.io/molpathR/)
[](https://CRAN.R-project.org/package=molpathR)
[](https://app.codecov.io/gh/CTTIR/molpathR?branch=main)
[](https://cran.r-project.org/package=molpathR)
[](https://cran.r-project.org/package=molpathR)
[](https://opensource.org/licenses/MIT)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 7,
fig.height = 5
)
```
## Installation
Install molpathR from GitHub:
```{r install, eval = FALSE}
# install.packages("remotes")
remotes::install_github("cttir/molpathR")
```
## Quick start
Load the package and create an example database:
```{r load}
library(molpathR)
db <- mp_example_db(n_patients = 50, seed = 42)
db
```
## Explore the data
Get a cohort summary:
```{r summary}
mp_summary(db)
```
## Query patients
```{r query}
# Find melanoma patients over 60
melanoma <- mp_query_patients(db, diagnosis == "Melanoma", age > 60)
head(melanoma)
```
## Query variants
```{r variants}
# Pathogenic TP53 variants with VAF > 10%
tp53 <- mp_query_variants(db, genes = "TP53", classification = "Pathogenic", min_vaf = 0.1)
head(tp53)
```
## Visualize
```{r landscape, fig.width = 8, fig.height = 5, fig.alt = "Recorded variant classifications across synthetic patients for the ten most frequent genes."}
mp_plot_variant_landscape(db, top_n = 10)
```
```{r survival, fig.width = 7, fig.height = 5, fig.alt = "Kaplan-Meier curves by diagnosis for synthetic overall survival times measured in months."}
mp_plot_survival(db, group_by = "diagnosis", type = "os")
```
## Launch the Shiny app
```{r shiny, eval = FALSE}
mp_run_app(db)
```
