Introduction to differential binding

ChIP-seq with Bioconductor in R

Peter Humburg

Statistician, Macquarie University

ChIP-seq with Bioconductor in R

Comparing samples

  • Two groups of samples: Primary and treatment resistant tumor.

Questions we would like to answer:

  • Are samples from the same group generally similar?
  • Are samples from different groups different?
  • What are those differences?
ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

PCA plots for ChIP-seq data

qc_result <- ChIPQC("sample_info.csv", "hg19")

counts <- dba.count(qc_results, summits=250)

plotPrincomp(counts)
ChIP-seq with Bioconductor in R

Hierarchical clustering

Compute distance between samples

distance <- dist(t(coverage))

Create dendogram

dendro <- hclust(distance)

Plot dendrogram

plot(dendro)
ChIP-seq with Bioconductor in R

Heatmaps

Create heatmap from coverage data for peaks

dba.plotHeatmap(peaks, maxSites = peak_count, correlations = FALSE)

ChIP-seq with Bioconductor in R

Let's practice!

ChIP-seq with Bioconductor in R

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