Question: rtracklayer::liftOver parameters (minMatch)
0
gravatar for Nik dAK
20 months ago by
Nik dAK10
Nik dAK10 wrote:

I have a question regarding the parameters available at the command line version but not in R.

Is there a possibility to for example alter the minMatch value (Minimum ratio of bases that must remap)?

Apparently this value adapts automatically from 0.95 default to 0.1 when using a chain for different species (in my case hg19ToMm10.over.chain) in R like it does on the webpage.

Anyways it would be great to manually adjust this value in R.

(I am aware that pslMap is maybe a better idea)

Thanks!

Best wishes,

Nik

 

ADD COMMENTlink modified 20 months ago by Michael Lawrence11k • written 20 months ago by Nik dAK10
Answer: rtracklayer::liftOver parameters (minMatch)
0
gravatar for Michael Lawrence
20 months ago by
United States
Michael Lawrence11k wrote:

I could look into it, but no promises. The rtracklayer liftOver is a complete reimplementation of the UCSC liftover tool, which is only freely available for academic use. I've avoided even looking at the liftover source code.

ADD COMMENTlink written 20 months ago by Michael Lawrence11k
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