On Tue, Apr 13, 2010 at 3:35 AM, margherita mutarelli < [email protected]> wrote:
> Dear all, > > please apologize if I missed this information, but I have looked throughout > the documentation and vignettes of the IRanges packages and I could not > find > this information: > > are the coordinates in IRanges objects considered as "0-indexed" or > "1-indexed"? > > I.e. when importing the refGene.txt table (or any) from UCSC, we know that > they are 0-indexed, meaning that the first base is not part of the > gene/transcript/object. > If IRanges are 1-index this means we have to subtract 1 from the start > coordinate precedent in the table when creating an IRanges object from > them. > > When used as indices into a sequence, they are treated as 1-based. This comes simply from all indexing in R being 1-based. Btw, with packages like rtracklayer and GenomicFeatures, you probably do not need to be manually importing data like the example above. > Is it correct? > This can be important to clarify, both when considering overlap of features > and in junctions, since it can shift the correct exon boundaries. > > Cheers, > > Margherita > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
