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ChIP-seq met Bioconductor in R

Peter Humburg

Statistician, Macquarie University

Gviz gebruiken

Wat plotten we?

Coördinaten instellen

library(Gviz)

ideogram <- IdeogramTrack("chr12", 
                          "hg19")

axis <- GenomeAxisTrack()

plotTracks(list(ideogram, axis), 
           from=101360000, 
           to=101380000)

Data toevoegen

cover_track <- DataTrack(cover_ranges,window=100000,type='h',name="Coverage")
plotTracks(list(ideogram, cover_track, axis), from=101360000, to=101380000)

Annotaties toevoegen

peak_track <- AnnotationTrack(peaks, name="Peaks")
plotTracks(list(ideogram, cover_track, peak_track, axis), 
           from=101360000, to=101380000)

Genannotaties

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

tx <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg19.knownGene, chromosome="chr12", 
                      start=101360000, end=101380000, name="Genes")
plotTracks(list(ideogram, cover_track, peak_track, tx, axis),
           from=101360000, to=101380000)

Laten we oefenen!

ChIP-seq met Bioconductor in R