# 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
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
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
library(devtools)
install_github("vjcitn/rhdf5client")
```
## Dependencies
To run the code you need:
- `GEOquery`
- `rhdf5client`
- `phantasuslite`
``` r
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
ess <- getGEO("GSE53053")
es <- ess[[1]]
```
ExpressionSet from the GEO doesn’t contain the expression matrix –
`exprs(es)` is empty.
``` r
head(exprs(es))
```
## GSM1281300 GSM1281301 GSM1281302 GSM1281303 GSM1281304 GSM1281305
## GSM1281306 GSM1281307
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))
```
## GSM1281300 GSM1281301 GSM1281302 GSM1281303 GSM1281304
## ENSMUSG00000000001 1015 603 561 549 425
## ENSMUSG00000000003 0 0 0 0 0
## ENSMUSG00000000028 109 34 0 14 9
## ENSMUSG00000000031 0 18 0 0 0
## ENSMUSG00000000037 0 0 0 0 0
## ENSMUSG00000000049 0 0 0 0 0
## GSM1281305 GSM1281306 GSM1281307
## ENSMUSG00000000001 853 407 479
## ENSMUSG00000000003 0 0 0
## ENSMUSG00000000028 165 0 15
## ENSMUSG00000000031 0 0 0
## ENSMUSG00000000037 0 0 0
## ENSMUSG00000000049 0 0 0
The available gene annotations are also filled in:
``` r
head(fData(es))
```
## Gene symbol ENSEMBLID
## ENSMUSG00000000001 Gnai3 ENSMUSG00000000001
## ENSMUSG00000000003 Pbsn ENSMUSG00000000003
## ENSMUSG00000000028 Cdc45 ENSMUSG00000000028
## ENSMUSG00000000031 H19 ENSMUSG00000000031
## ENSMUSG00000000037 Scml2 ENSMUSG00000000037
## ENSMUSG00000000049 Apoh ENSMUSG00000000049
