data(exampleDataSet,package="JctSeqData");
plotMA(jscs);
## Not run:
# ########################################
# #Set up example data:
# decoder.file <- system.file(
# "extdata/annoFiles/decoder.bySample.txt",
# package="JctSeqData");
# decoder <- read.table(decoder.file,
# header=TRUE,
# stringsAsFactors=FALSE);
# gff.file <- system.file(
# "extdata/cts/withNovel.forJunctionSeq.gff.gz",
# package="JctSeqData");
# countFiles <- system.file(paste0("extdata/cts/",
# decoder$sample.ID,
# "/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz"),
# package="JctSeqData");
# ######################
# #Run example analysis:
# jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
# sample.names = decoder$sample.ID,
# condition=factor(decoder$group.ID),
# flat.gff.file = gff.file,
# analysis.type = "junctionsAndExons"
# );
# ########################################
#
# #Plot M-A:
# plotMA(jscs);
#
# ## End(Not run)
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