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The import_hitchip function imports HITChip phylogenetic microarray data from a given HITChip data folder into phyloseq format. The pull request has been previously discussed with joey711 by email and I have now completed it in the hope that it will provide a useful starting point for expanding phyloseq capabilities to better cover phylogenetic microarrays.
If this pull request cannot be accepted for any reason, I will then maintain these functions in the microbiome R package instead. But I feel it would better fit the phyloseq package.