R/testit.R

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

opt <- list()
opt$chromstarObject <- '~/bioinformatics/galaxy/tools/chromstaR-galaxy/test-data/output_chromstaR-result.rdata'
opt$annotationBed6 <- '~/bioinformatics/galaxy/tools/chromstaR-galaxy/test-data/rn4_protein_coding_genes.bed'
opt$bpAroundAnnotation <- 10000
opt$numIntervals <- 20
opt$statistic <- "fold"
opt$numLoci <- 1000

opt <- list()
opt$chromstarObject <- '~/bioinformatics/galaxy/tools/chromstaR-galaxy/test-data/output_chromstaR-result.rdata'
opt$changeWhat <- 'changePostCutoff'
opt$cutoff <- 0.9999999

opt$differentialScore <- 0.9999
opt$minWidth <- 300
opt$differentialPosterior <- 0.9999