README.rmd

---
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# PhantasusLite

PhantasusLite -- a tool designed to integrate the work with RNA-Seq count matrices into a single and fast R-pipeline. This R-package supports loading the data from GEO by GSE. It provides url access to the remote repository with the archs4, archs4_zoo and dee2 HDF5-files for getting the count matrix. Finally phantasusLite allows to get an ExpressionSet with the expression matrix for future differential expression analysis.

## Installation

It is recommended to install the release version of the package from Bioconductor using the following commands:

```{r eval=FALSE}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phantasusLite")
```

Alternatively, the most recent version of the package can be installed from the GitHub repository:

```{r message=FALSE, eval=FALSE}
library(devtools)
install_github("ctlab/phantasusLite")
```

Note that the latest version depends on `rhdfclient5 >= 1.25.1` from Bioconductor 3.19, which on older systems can be more convenient to install from GitHub:

```{r message=FALSE, eval=FALSE}
library(devtools)
install_github("vjcitn/rhdf5client")
```

## Dependencies

To run the code you need:

-   `GEOquery`
-   `rhdf5client`
-   `phantasuslite`

```{r message=FALSE, warning=FALSE}
library(GEOquery)
library(rhdf5client)
library(phantasusLite)
```


## Quick start

To run the package enter the code sample below.

Let's load the ExpressionSet from GEO

```{r message=FALSE}
ess <- getGEO("GSE53053")
es <- ess[[1]]
```


ExpressionSet from the GEO doesn't contain the expression matrix -- `exprs(es)` is empty.

```{r}
head(exprs(es))
```

Function loadCountsFromHSDS returns an ExpressionSet with the expression matrix -- now `exprs(es)` contains an expression matrix. The default remote repository URL is '<https://alserglab.wustl.edu/hsds/?domain=/counts>'.

```{r}
# `url` is explicitly specified for illustration purposes and can be omitted
es <- loadCountsFromHSDS(es, url = 'https://alserglab.wustl.edu/hsds/?domain=/counts')
head(exprs(es))
```


The available gene annotations are also filled in:
```{r}
head(fData(es))
```