## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- library(EBSEA) data("exonCounts") head(exonCounts) ## ----------------------------------------------------------------------------- filtCounts <- filterCounts(exonCounts) ## ----------------------------------------------------------------------------- group <- data.frame('group' = as.factor(c('G1', 'G1', 'G1', 'G2', 'G2', 'G2', 'G2'))) row.names(group) <- colnames(filtCounts) design <- ~group ebsea.out <- EBSEA(filtCounts, group, design) ## ----------------------------------------------------------------------------- group <- data.frame('group' = as.factor(c('G1', 'G1', 'G1', 'G2', 'G2', 'G2', 'G2')), 'paired' = as.factor(c(1,2,3,1,2,3,3))) row.names(group) <- colnames(exonCounts) design <- ~paired+group ebsea.out <- EBSEA(exonCounts, group, design) ## ----------------------------------------------------------------------------- head(ebsea.out$ExonTable) ## ----------------------------------------------------------------------------- head(ebsea.out$GeneTable) ## ----fig.width = 6, fig.height= 6--------------------------------------------- visualizeGenes('FBgn0000064', ebsea.out)