Category Archives: Update

Correct coordinates in gtfToBed()

Aki Nakao pointed out a problem in gtfToBed(). In earlier versions the function did a basic reformatting without adjusting the coordinate system between gtf and bed (gtf is 1-based, bed however is 0-based). The function got now the option correctBases=TRUE … Continue reading

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Missing dependency

No idea how a missing dependency could sneak its way into the package, but still parallel:detectCores() was not imported from the package. This bug is now fixed in 0.2.9.2.

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Bugfix in eQTL/QTL

There was a bug in the joinEQTL() subfunction. If no SNPs were in the window to be tested for eQTL, the joining got haywired and threw an error. This is not fixed in developer release version 0.2.9.1

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Better package structure

In order to maintain a better structure of the package, I ‘outsourced’ today all the I/O functions into a separate R-package called GenomicTools.fileHandler. That way I hope to get a better structure into my packages, as some I/O functions are … Continue reading

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Input checks improved

The importGTF() function received today some import option checks to make it easier to use/trace mistakes.

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Updates in QTL() function

The QTL function accepts now also matrices and vectors as input fot the genotypes.

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importFeatureCounts() function added

A new function to import the output of featureCOunts to R has been added.

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New option in importGTF()

The importGTF() function has now an option to define numeric values during the import. This makes it easier to import expression data in gtf format. By default FPKM and TPM are imported as numeric values, but also other feature names … Continue reading

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New function prereadGTF()

The function prereadGTF() was added to the package. The function reads in by default the first 1000 rows of a gtf and summarizes the content in a way that the inforamtion is needed to import the GTF properly. For that … Continue reading

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Semicolon issue in importGTF() fixed

When the last feature in V9 of importGTF() was requested, the ending semicolon was not removed. This issue is resolved and the semicolon is removed now during the import.

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