## ----echo=FALSE,include=FALSE------------------------------------------------- library(yarn) data(skin) ## ----------------------------------------------------------------------------- skin ## ----checkMisAnnotation------------------------------------------------------- checkMisAnnotation(skin,"GENDER",controlGenes="Y",legendPosition="topleft") ## ----checkTissuesToMerge------------------------------------------------------ checkTissuesToMerge(skin,"SMTS","SMTSD") ## ----filterGenes-------------------------------------------------------------- skin_filtered = filterLowGenes(skin,"SMTSD") dim(skin) dim(skin_filtered) ## ----filter------------------------------------------------------------------- tmp = filterGenes(skin,labels=c("X","Y","MT"),featureName = "chromosome_name") # Keep only the sex names tmp = filterGenes(skin,labels=c("X","Y","MT"),featureName = "chromosome_name",keepOnly=TRUE) ## ----density------------------------------------------------------------------ plotDensity(skin_filtered,"SMTSD",main=expression('log'[2]*' raw expression')) skin_filtered = normalizeTissueAware(skin_filtered,"SMTSD") plotDensity(skin_filtered,"SMTSD",normalized=TRUE,main="Normalized") ## ----------------------------------------------------------------------------- data(skin) res = plotCMDS(skin,pch=21,bg=factor(pData(skin)$SMTSD)) ## ----------------------------------------------------------------------------- filtData = filterLowGenes(skin,"SMTSD") plotDensity(filtData,groups="SMTSD",legendPos="topleft") ## ----------------------------------------------------------------------------- library(RColorBrewer) tissues = pData(skin)$SMTSD heatmapColColors=brewer.pal(12,"Set3")[as.integer(factor(tissues))] heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50) plotHeatmap(skin,normalized=FALSE,log=TRUE,trace="none",n=10, col = heatmapCols,ColSideColors = heatmapColColors,cexRow = 0.25,cexCol = 0.25) ## ----------------------------------------------------------------------------- sessionInfo()