Rseasnap

A collection of functions which make it easy to access the files and objects created by the sea-snap DE pipeline.

Why Rseasnap:

• shortcuts for accessing pipeline objects
• produce plots on the fly
• easier to work with multiple pipelines

Why not part of sea-snap distribution (e.g. as R scripts):

• better documentation
• can be used for other tasks as well
• easier to maintain

Installation

You can install the current version of Rseasnap as follows:

library(devtools)
install_github("bihealth/Rseasnap")

Alternatively, clone the git repo and install from the clone directory, e.g.

system("git clone [email protected]:bihealth/Rseasnap.git")
devtools::install_git("Rseasnap")

Quickstart

Load the DE pipeline object:

library(Rseasnap)
pip <- load_de_pipeline("DE_config.yaml")

Once the YAML file is loaded into the object, you can use it to access various objects and files:

# get the counts
counts <- get_counts(pip)

# get the expression data
expr <- get_exprs(pip)

# show contrast names
get_contrast_names(pip)

# get the DE results
res <- get_contrasts(pip)

# get the gene annotation file
annot <- get_annot(pip)

# get the covariate file
covar <- get_covariates(pip)