News:New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps

Question

[Rory Stark]

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)

[K_QIN]

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

[Rory Stark]

This issue has been logged as Diffbind:dba.plotProfile error: each range must have an end that is greater or equal to its start minus one and is being addressed there.

[Ian.kouzel]

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'

[Rory Stark]

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.

[Rylee]

Hi Rory, I'm also getting the same error with non-human/mouse samples. Has this been addressed?

dbs$config$RunParallel <- FALSE

profiles <-dba.plotProfile(dbs)

returns:

Warning in if (pv$config$AnalysisMethod == DBA_EDGER) { : \ the condition has length 1 and only the first element will be used\ Generating report-based DBA object...\ Warning in scores <= th :\ longer object length is not a multiple of shorter object length\ Generating profiles...\ Error in value[3L] : \ profileplyr error: Error: BiocParallel errors\ 1 remote errors, element index: 1\ 5 unevaluated and other errors\ first remote error: found no sequence renaming map compatible with seqname style "NCBI" for this object

I am using DeSeq2 for analysis, so not sure if the error is arising from the DBA_EDGER method call.

[ipsc-jl]

Hello, I'm getting this error when trying to use dba.plotProfile:

Error in value[3L] : profileplyr error: Error: stop worker failed: wrong args for environment subassignment

Do you know how I can get around this issue? Thank you!

[Rory Stark]

I have not seen this error before. Perhaps try running in serial (not parallel) mode and we can see a clearer error message?