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KanduriC / GenomeBuildPredictor

Predicts the genome build version of genomic track files, if any of the sequence coordinates in the input track file are unique to a genome build version
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Determining 23andme file genome build fails #1

Open rduque1 opened 7 years ago

rduque1 commented 7 years ago

Hi,

I transfromed using plink a 23andme file to bed format, but when I try to get the genome build I get an error message Error: $ operator is invalid for atomic vectors. To transform the 23andme file to bed I did plink --23file <23andmefile> --make-bed --out test3

> mytrack <- import_genomic_track('test3.bed',file_format = 'bed')
Error: $ operator is invalid for atomic vectors

I tried with another 23andme file too and got the same error. When I try with the example bed file on the homepage it works.

KanduriC commented 7 years ago

Hi,

The import_genomic_track function internally uses the rtracklayer package (http://bioconductor.org/packages/release/bioc/html/rtracklayer.html) to parse genomic track file formats. In our experience, the parsing fails, if the file formats do not strictly adhere to the file format specifications. As a quick diagnosis, you can check whether you are able to import the bed file using rtracklayer.

Best, Chakri