matrix is NULL in output of readVCFToMatrixByGene

[yiming wu]

Dear developers,

I am new to seqminer and I want to use it prepare genotype matrix for SKAT.

I have used ANNO to annotate my vcf file and prepared geneFile (refFlat_hg19.txt.gz).

After running 'readVCFToMatrixByGene' for several particular genes, I can got results, but only sample IDs in the list, not genotype sore matrix there.

like num[0, 1:340], 340 is my sample size.

I also tested reading by range and set a very long range chr:1-1000000, but I can't get matrix still.

Can you please tell me what's the issue in my process probably?

I have two more questions about the function of 'readVCFToMatrixByGene'.

1, how to take a list of genes as input, rather than specify one gene in parameters each time.

2, in manual file, it says the annoType can be left empty, but I got this error "argument "annoType" is missing, with no default" when I leave it blank or nothing in quote "".

Thank you for your help.

regards

Yiming