ChIP-seq with Bioconductor in R
Peter Humburg
Statistician, Macquarie University
Counting reads in peak set:
peak_counts <- dba.count(qc_output, summits=250)
Creating a contrast:
peak_counts <- dba.contrast(peak_counts, categories = DBA_CONDITION)
Other supported categories:
bind_diff <- dba.analyze(peak_counts)
PCA plot for differentially bound peaks
dba.plotPCA(bind_diff, DBA_Condition, contrast=1)
Heatmap for differentially bound peaks
dba.plotHeatmap(bind_diff, DBA_Condition, contrast=1)
ChIP-seq with Bioconductor in R