Tools for analysis of Schizosaccharomyces splicing microarray

Example workflow

# import libraries
library(sma)
library(GenomicFeatures)
library(limma)

# set up working directories
setwd("path_to_data")
# create a directory called "raw" in "path_to_data"
# put your raw .gpr files there
target_path <- "./data/targets.txt"
load("./data/annotation.RData")
load("./data/features.RData")

# load and normalize data
e <- sma.load(target_path)

# analyze data using the E*I/J score
results <- sma.analyze(e)

# model intron features based on microarray classification
models <- sma.model(results$stats, features)