pharm_gen.Rmd

---
title: "CANDLEfun for pharmacogenomics"
author: "US"
date: "`r doc_date()`"
abstract: >
  Overview of pharmacogenomics datasets and papers.
output: 
  BiocStyle::html_document:
    df_print: paged
    keep_md: TRUE
bibliography: references.bib
nocite: | 
  @Karczewski2012-yy; @Hafner2017-jw; @Wheeler2013-dn; @El-Hachem2017-cc; @Zhang2015-kx; @Goodspeed2016-jv; @Madhukar2017-fe; @Gayvert2016-zi
---

```{r include=FALSE}
library(knitr)
opts_chunk$set(warning=FALSE, message=FALSE, tidy=TRUE)
```

# Resources

## [Pharmacodb]

```{r}
library(dplyr)
pdb = src_mysql('pharmacodb', host='solexadb.cpmth1vkdqqx.us-east-1.rds.amazonaws.com', user='deeplearn', password = 'deeplearn')
```

Tables available include:

```{r}
pdb_t = sapply(db_list_tables(pdb$con),function(tblname) tbl(pdb, tblname), USE.NAMES = TRUE, simplify = FALSE)
names(pdb_t)
```

Datasets include:

```{r}
pdb_t$datasets %>% left_join(pdb_t$source_statistics,c("dataset_id" = "id")) %>% knitr::kable()
```

[Pharmacodb]: http://pharmacodb.pmgenomics.ca/

# References