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:

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:

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:

library(devtools)
install_github("vjcitn/rhdf5client")

Dependencies

To run the code you need:

• GEOquery
• rhdf5client
• phantasuslite

library(GEOquery)
library(rhdf5client)
library(phantasusLite)

Quick start

To run the package enter the code sample below.

Let’s load the ExpressionSet from GEO

ess <- getGEO("GSE53053")
es <- ess[[1]]

ExpressionSet from the GEO doesn’t contain the expression matrix – exprs(es) is empty.

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’.

# `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:

head(fData(es))

##                    Gene symbol          ENSEMBLID
## ENSMUSG00000000001       Gnai3 ENSMUSG00000000001
## ENSMUSG00000000003        Pbsn ENSMUSG00000000003
## ENSMUSG00000000028       Cdc45 ENSMUSG00000000028
## ENSMUSG00000000031         H19 ENSMUSG00000000031
## ENSMUSG00000000037       Scml2 ENSMUSG00000000037
## ENSMUSG00000000049        Apoh ENSMUSG00000000049