data(tamoxifen_peaks)
# peak overlap correlation heatmap
dba.plotHeatmap(tamoxifen)
data(tamoxifen_counts)
# counts correlation heatmap
dba.plotHeatmap(tamoxifen)
data(tamoxifen_analysis)
#correlation heatmap based on all normalized data
dba.plotHeatmap(tamoxifen,contrast=1,th=1)
#correlation heatmap based on DB sites only
dba.plotHeatmap(tamoxifen,contrast=1)
#binding heatmap based on DB sites
dba.plotHeatmap(tamoxifen,contrast=1,correlations=FALSE)
#binding heatmap based on 1,000 sites with highest variance
sites <- dba.plotHeatmap(tamoxifen,contrast=1,th=1,
correlations=FALSE,sortFun=var)
sites
data(tamoxifen_counts)
#Examples of heatmaps using DB sites with different subsets of samples
#exclude T47D
tamoxifen <- dba.contrast(tamoxifen,tamoxifen$masks$Resistant,c(3:5,10:11))
tamoxifen <- dba.analyze(tamoxifen,bCorPlot=FALSE)
# regular heatmaps with two contrast groups
dba.plotHeatmap(tamoxifen, contrast=1)
#also include the T47D samples
dba.plotHeatmap(tamoxifen,contrast=1,mask=tamoxifen$masks$All)
#correlation heatmap without MCF7
plot(tamoxifen,contrast=1,mask=!tamoxifen$masks$MCF7)
# binding heatmap using only the MCF7 samples
dba.plotHeatmap(tamoxifen,contrast=1,mask=tamoxifen$masks$MCF7,correlations=FALSE)
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