News:New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
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Rory Stark ★ 4.6k
@rory-stark-5741
Last seen 5 days ago
CRUK, Cambridge, UK

For DiffBind users, there is a new function in Bioconductor 3.13, dba.plotProfile(), that makes it straightforward to calculate peak profiles and generate complex heatmap plots.

dba.plotProfile() flexibly packages different sets of sites and samples from a DiffBind analysis for the Bioconductor package profileplyr (by Tom Carroll and Doug Barrows), generating profileplyr objects that can be customized using that package, including exporting to deepTools.

A tutorial in the form of a markdown workbook is available, showing how to use the dba.plotProfile() function. For example, using the vignette tamoxifen dataset, the following plot can be generated with one simple call:

profiles <- dba.plotProfile(tamoxifen, doPlot=TRUE)

Default profile plot from `dba.plotProfile()` using sample analysis

profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq • 1.4k views
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This looks great! Is there a way to adjust the +/- 1500 window size?

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Yes, you have full control over the windows by passing through parameters to profileplyr::BamBigwig_to_chipProfile(), such as style, distanceAround, nOfWindows, and bin_size.

If you look at the tutorial linked in the original post, Section 7 explains how to control the windows.

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Hi, I really appreciate your update and comments. One question - can I reverse gain and loss locations?

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If you could ask this as a question on the main support forum (instead of here in News), I'd be happy to give a detailed answer on how to do this.

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Thank you so much! I'll post the question there.

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