Category Archives: Update
There was a problem with the rows of interest identification in the function, as I did not use REGEX to identify the line starts. This I fixed now in the new version 0.3.1.
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.
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
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.
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
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
Input checks improved
The importGTF() function received today some import option checks to make it easier to use/trace mistakes.
Updates in QTL() function
The QTL function accepts now also matrices and vectors as input fot the genotypes.
importFeatureCounts() function added
A new function to import the output of featureCOunts to R has been added.
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