News:New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
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4 months ago
Rory Stark ★ 1.2k

For users of the Bioconductor package DiffBind, 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

DiffBind ChIP-seq deepTools visualization ATAC-seq • 835 views
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Hi, I am using the new plotProfile function of Diffbind to create some graphs, and get the following error with one subset of my data:

dbObj$config$RunParallel <- TRUE

profiles <- dba.plotProfile(dbObj)

Generating report-based DBA object... Generating profiles... Error in value[3L] : profileplyr error: Error: BiocParallel errors element index: 2 first error: each range must have an end that is greater or equal to its start minus one

All the rest of the ChIPQC and Diffbinds works smoothly. Also the other four samples of the same dataset worked as well (I processed them separately, as they were different treatments). What could be the problem?

Thanks, KQ2012

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Hi, is it possible to use dba.plotProfile to plot samples other than mouse/human using custom gene models? When I tried to plot my samples, I got 'first error: found no sequence renaming map compatible with seqname style "NCBI" for this object'

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Hmmn, I'm not sure where that is coming from. In the released version of dba.plotProfile(), there shouldn't be any dependencies on the reference genome or gene model. I'd like to track down what is going on!

Could you include a) the software versions you are using, and b) the calls you are making and their output? Please set DBA$config$RunParallel <- FALSE so all the warnings/errors are shown in order.

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