### R code from vignette source 'ExCluster.Rnw' ################################################### ### code chunk number 1: ExCluster.Rnw:186-191 ################################################### library(ExCluster) # load the sub-sampled GTF file path from the ExCluster package GTF_file <- system.file("extdata","sub_gen.v23.gtf", package = "ExCluster") # now run GTF\_file without assigning a GFF\_file to write out, assigning the results to the GFF object GFF <- GFF_convert(GTF.File=GTF_file) ################################################### ### code chunk number 2: ExCluster.Rnw:198-206 ################################################### # specify the path to the ExCluster package ExClust_Path <- system.file(package="ExCluster") # now find the bam files within that folder bamFiles <- list.files(ExClust_Path,recursive=TRUE,pattern="*.bam",full.names=TRUE) # assign sample names (only 2 replicates per condition in this example) sampleNames <- c("iPSC_cond1_rep1","iPSC_cond1_rep2","iPSC_cond2_rep1","iPSC_cond2_rep2") # now run processCounts, with paired.Reads=TRUE because we are counting paired-end data normCounts <- processCounts(bam.Files=bamFiles, sample.Names=sampleNames, annot.GFF=GFF, paired.Reads=TRUE) ################################################### ### code chunk number 3: ExCluster.Rnw:213-219 ################################################### # assign condition numbers to your samples (we have 4 samples, 2 replicates per condition) condNums <- c(1,1,2,2) # now we run ExCluster, assigning its output to the ExClustResults variable # we are not writing out the ExClustResults table, nor are we plotting exons # we also use combine.Exons=FALSE to discover one 'significant' gene for example plot purposes ExClust_Results <- ExCluster(exon.Counts=normCounts,cond.Nums=condNums,annot.GFF=GFF, combine.Exons=FALSE) ################################################### ### code chunk number 4: ExCluster.Rnw:226-231 ################################################### # now we must specify a directory to write images to # here we use tempdir, but you may substitute another folder path if you wish outDir <- paste(tempdir(),"/Images/",sep="") # now we can run our exon log2FC plotting function plotExonlog2FC(results.Data=ExClust_Results, out.Dir=outDir, plot.Type="PNG") ################################################### ### code chunk number 5: ExCluster.Rnw:243-244 ################################################### GRanges.ExClustResults <- GRangesFromExClustResults(results.ExClust=ExClust_Results)