[R] Package Seqminer: Fundamental usage question

Darren Obbard darren.obbard at ed.ac.uk
Fri May 10 17:30:15 CEST 2013


I am trying to use the package 'SeqMiner" zhanxw.com/seqminer/, and I 
would like to use any of the functions
or readVCFToListByRange()

I have run the example code on the test datasets, and have got the 
expected output.

Using my own data, I always get back empty matrices (in the case of the 
first two functions) , or a list of empty components (with the second 
two functions)

My input is a tabix-indexed bgzipped vcf file that has been annotated by 
TabAnno, and a refFlat file (as requested).

The call readVCFToMatrixByGene(fileName="MyVXF", fileName="MyrefFlat", 
fileName="MyName", annoType="Synonymous") throws no errors.

This at least suggests that "MyName" is correctly identified in both files.

The matrix returned is empty, although with correct sample names 
(suggesting that the samples are correctly identified)

I have tried all annotypes (annoType="Synonymous", etc), and none of 
them give me any result.

Has anyone ever successfully used this package? and if so, would they be 
willing to correspond on how to use it?

Thanks in advance for any advice,


Darren Obbard

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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