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.
The importGTF() function received today some import option checks to make it easier to use/trace mistakes.
The QTL function accepts now also matrices and vectors as input fot the genotypes.
A new function to import the output of featureCOunts to R has been added.
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 can be given to the new option num.features
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 the different available levels in column three are displayed as well as the different features per level in column 9.
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.
The importGTF() function can now also import several gtf and merge them into one
output file. Further, the function offers now verbose feedback (if requested
with the verbose=TRUE option).
Another change is the skip option, previously the default was to skip the first 5
rows, now the default is ‘auto’. In auto mode all rows that start with ‘#’ are
The package description in ‘Computer Methods and Programs in Biomedicine’ was published here.
Until 23.10.2017 it can be downloaded here.