VCFArray is a Bioconductor package that represents VCF files as objects
derived from the
DelayedArray package and
It converts data entries from VCF file into a DelayedArray-derived
data structure. The backend VCF file could either be saved on-disk
locally or remote as online resources. Data entries that could be
extracted include the fixed data fields (REF, ALT, QUAL, FILTER),
information field (e.g., AA, AF...), and the individual format field
(e.g., GT, DP...). The array data generated from fixed/information
fields are one-dimensional
VCFArray, with the dimension being the
length of the variants. The array data generated from individual
"FORMAT" field are always returned with the first dimension being
"variants" and the second dimension being "samples". This feature
is consistent with the assay data saved in
and makes the
VCFArray package interoperable with other established
Bioconductor data infrastructure.
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