## ----loadmethods, echo=FALSE, message=FALSE, warning=FALSE--------------- library(methods) ## ----installme, eval=FALSE----------------------------------------------- # source("http://bioconductor.org/biocLite.R") # biocLite("ballgown") ## ----makebgobj, message=FALSE-------------------------------------------- library(ballgown) data_directory = system.file('extdata', package='ballgown') # automatically finds ballgown's installation directory # examine data_directory: data_directory # make the ballgown object: bg = ballgown(dataDir=data_directory, samplePattern='sample', meas='all') bg ## ----struct-------------------------------------------------------------- structure(bg)$exon structure(bg)$intron structure(bg)$trans ## ----getexpr------------------------------------------------------------- transcript_fpkm = texpr(bg, 'FPKM') transcript_cov = texpr(bg, 'cov') whole_tx_table = texpr(bg, 'all') exon_mcov = eexpr(bg, 'mcov') junction_rcount = iexpr(bg) whole_intron_table = iexpr(bg, 'all') gene_expression = gexpr(bg) ## ----pData--------------------------------------------------------------- pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10)) ## ----indexex------------------------------------------------------------- exon_transcript_table = indexes(bg)$e2t transcript_gene_table = indexes(bg)$t2g head(transcript_gene_table) phenotype_table = pData(bg) ## ----dirs---------------------------------------------------------------- head(bg@dirs) ## ----mergedDate---------------------------------------------------------- bg@mergedDate ## ----meas---------------------------------------------------------------- bg@meas ## ----plotTranscripts, fig.height=8, fig.width=8, fig.cap=""-------------- plotTranscripts(gene='XLOC_000454', gown=bg, samples='sample12', meas='FPKM', colorby='transcript', main='transcripts from gene XLOC_000454: sample 12, FPKM') ## ----plotTranscripts2, fig.height=10, fig.width=10, fig.cap=""----------- plotTranscripts('XLOC_000454', bg, samples=c('sample01', 'sample06', 'sample12', 'sample19'), meas='FPKM', colorby='transcript') ## ----plotMeans, fig.height=5, fig.width=10, fig.cap=""------------------- plotMeans('XLOC_000454', bg, groupvar='group', meas='FPKM', colorby='transcript') ## ----stattest------------------------------------------------------------ stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='group') head(stat_results) ## ----stattest_time------------------------------------------------------- pData(bg) = data.frame(pData(bg), time=rep(1:10, 2)) #dummy time covariate timecourse_results = stattest(bg, feature='transcript', meas='FPKM', covariate='time', timecourse=TRUE) ## ----stattest_adjust----------------------------------------------------- group_adj_timecourse_results = stattest(bg, feature='transcript', meas='FPKM', covariate='time', timecourse=TRUE, adjustvars='group') ## ----customMod----------------------------------------------------------- # create example data: set.seed(43) sex = sample(c('M','F'), size=nrow(pData(bg)), replace=TRUE) age = sample(21:52, size=nrow(pData(bg)), replace=TRUE) # create design matrices: mod = model.matrix(~ sex + age + pData(bg)$group + pData(bg)$time) mod0 = model.matrix(~ pData(bg)$group + pData(bg)$time) # run differential expression tests: adjusted_results = stattest(bg, feature='transcript', meas='FPKM', mod0=mod0, mod=mod) head(adjusted_results) ## ----cluster------------------------------------------------------------- clusterTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans') ## ----clusterviz, fig.height=8, fig.width=8, fig.cap=""------------------- plotLatentTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans', returncluster=FALSE) ## ----collapse------------------------------------------------------------ agg = collapseTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans') stattest(gowntable=agg$tab, pData=pData(bg), feature='transcript_cluster', covariate='group', libadjust=FALSE) ## ----sessioninfo, results='markup'--------------------------------------- sessionInfo()