No, I forgot to attach the file. Here is the link: https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan, These sound like great contributions. I didn't get an attachment - did you send one? Thanks. Valerie On 04/30/2014 01:06 PM, Ryan C. Thompson wrote:Hi all, I recently asked about ways to do non-standard read counting in summarizeOverlaps, and Martin Morgan directed me toward writing a custom function to pass as the "mode" parameter. I have now written the custom modes that I require for counting my ChIP-Seq reads, and I figured I would contribute them back in case there was interest in merging them. The main three functions are "ResizeReads", "FivePrimeEnd", and "ThreePrimeEnd". The first allows you to directionally extend or shorten each read to the effective fragment length for the purpose of determining overlaps. For example, if each read represents the 5-prime end of a 150-bp fragment and you want to count these fragments using the Union mode, you could do: summarizeOverlaps(mode=ResizeReads(mode=Union, width=150, fix="start"), ...) Note that ResizeReads takes a mode argument. It returns a function (with a closure storing the passed arguments) that performs the resizing (by coercing reads to GRanges and calling "resize") and then dispatches to the provided mode. (It probably needs to add a call to "match.fun" somewhere.) The other two functions are designed to count overlaps of only the read ends. They are implemented internally using "ResizeReads" with width=1. The other three counting modes (the "*ExtraArgs" functions) are meant to be used to easily construct new counting modes. Each function takes any number of arguments and returns a counting mode that works like the standard one of the same name, except that those arguments are passed as extra args to "findOverlaps". For example, you could do Union mode with a requirement for a minimum overlap of 10: summarizeOverlaps(mode=UnionExtraArgs(minoverlap=10), ...) Note that these can be combined or "nested". For instance, you might want a fragment length of 150 and a min overlap of 10: myCountingMode <- ResizeReads(mode=UnionExtraArgs(minoverlap=10), width=150, fix="start") summarizeOverlaps(mode=myCountingMode, ...) Anyway, if you think any of these are worthy of inclusion for BioConductor, feel free to add them in. I'm not so sure about the "nesting" idea, though. Functions that return functions (with states saved in closures, which are then passed into another function) are confusing for people who are not programmers by trade. Maybe summarizeOverlaps should just gain an argument to pass args to findOverlaps. -Ryan Thompson _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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