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.
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 so that by default one base is substracted from both, that start and the end coordinated to correct for the different coordinate systems
A new version (0.1.5.9) of the associated package
was just submitted to Cran. It fixes a few smaller bugs in the file handling of the suite.
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 proper summary and plot functions for the log files to process this huge amount of information.
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 other functions around it.
The function importFA() does not rely anymore on alternating rows between sequence and identifer, but can import now any kind of fasta file.
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.
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
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 into one data table
* importFeatureCounts() function added
* typo in ‘importPED()’ fixed
* Bug fixed in rearranged()
* QTL does now accept also plain vectors and matrices as input for genotypes
* importGTF issue fixed with auto separation detection from fread()
* improved input checks of importGTF()
* import* functions Deprecated and moved to the new package GenomicTools.fileHandler
* print.qtlRes handles now output without significant results
* bugfix in eqtlDir and eqtlLM (error, if only one SNP is tested)
* Couple of smaller bugfixes
* importVCF moved to GenomicTools.fileHandler
* No empty (=NA or NaN) p.values will be printed anymore in print.eqtl output
* Curtesy feedback for missing URl in getRSLocation
* getRSLocation URL adjusted to new Ensembl server adresses
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 also in the hoardeR package and so it was a bit tricky to find and/or use them. However, as this package is some kind of subpackage of GenomicTools, I’ll keep here the updates also for this package.
The corresponding files will be depreciated and removed from the corresponding packages then also in the next updates.