Overlapping features in a GTF annotation, such as overlapping exons from the same gene, are collapsed into a single feature that covers all overlapping features.
flattenGTF(GTFfile, GTF.featureType = "exon", GTF.attrType = "gene_id")
a character string giving the name of a GTF file as input.
a character string giving the feature type used to select rows in a GTF annotation.
a character string giving the attribute type in a GTF annotation which will be used to group features.
This function locates features in a GTF annotation via
GTF.featureType and then groups them into meta-features via
Default values of these two parameters will make exons be identified and then grouped into genes.
If there is overlap found between features belonging to the same meta-feature, this function will merge all overlaping features to form a single larger feature that covers all overlapping features.
Output of this function is a SAF format annotation which can be fed to
featureCounts function for read counting.
Description to SAF format annotation can also be found in
data.frame including a SAF format annotation.
Yang Liao and Wei Shi
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