Author Archives: fischuu

importVCF() improved

Today I improved the importVCF() function. Now, also the different INFO fields of a vcf are imported and are now also accessible. Further, in case of ‘A/B’ notation of genotypes, both variants A/B and B/A are now interpreted as 01.

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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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New Version

A new version (0.1.5.9) of the associated package GenomicTools.fileHandler was just submitted to Cran. It fixes a few smaller bugs in the file handling of the suite.

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importSTARLog() updated

I updated today the importSTARLog function so that it imports now both, the final.log and the log files. In addition, it can do that for all files within a folder and its subfolders. The next thing will be to write … Continue reading

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seqlength() function added

I added the seqlength() function to get the sequence length of a fa-object. This is in principle just a wrapper around the nchar() base-R command, but having an own function for this help then maybe later to write more sophisticated … Continue reading

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importFA() update

The function importFA() does not rely anymore on alternating rows between sequence and identifer, but can import now any kind of fasta file.

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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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New versions on Cran

Today the versions 0.2.8 for GenomicTools and 0.1.4 for GenomicTools.fileHandler have been released with a couple of bugfixes and a list of new features. In details we have * prereadGTF() function added * importGTF() function can now merge several gtfs … Continue reading

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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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