soGGi package: Error in .validate_names(rownames, ans_rownames, "assay rownames()"
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@nicolasdescostes-13127
Last seen 7 months ago

Hi,

I am following this tutorial: https://rockefelleruniversity.github.io/RUATACWorkshop.html

I tried the most recent version of soGGi but also the one of the tutorial (1.10.4).

When calculating:

nucFree <- regionPlot(bamFile = sortedBAM, testRanges = TSSs, style = "point", 
    format = "bam", paired = TRUE, minFragmentLength = 0, maxFragmentLength = 100, 
    forceFragment = 50)

I get the error:

Error in .validate_names(rownames, ans_rownames, "assay rownames()", "rowData rownames() / rowRanges names()") : 
  assay rownames() must be NULL or identical to rowData rownames() /
  rowRanges names()

I found that it has to do with "SummarizedExperiment": https://support.bioconductor.org/p/83850/

Can that be corrected in the package?

Thx

soggi • 544 views
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@nicolasdescostes-13127
Last seen 7 months ago

Adding this line to the code solved the issue:

profileMat <- RegionsMat
    colnames(profileMat) <- c(paste0("Point_Centre",seq(0-distanceUpStart,-1)),"Point_Centre",paste0("Point_Centre",seq(1,distanceDownEnd)))
    filteredRanges <- c(RangesPos,RangesNeg)

  ------->  ****names(filteredRanges) <- c(as.character(RangesPos$giID), as.character(RangesNeg$giID))****

    profileSample <- SummarizedExperiment(profileMat,rowRanges=filteredRanges[match(rownames(profileMat),filteredRanges$giID)])
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hi Nicolas,

Thank you for bug report (and adding a fix!)

I will update this in release and development tomorrow.

Thanks again,

tom

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@Nicolas, Thanks for the bug report and the fix. @Thomas, I submitted a pull request containing Nicolas' fix.

Best wishes

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Hello,

I am still getting the same error when I run the regionPlot function. Is there a way to go about fixing this?

Best, Sarah

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