NEWS.md
"short"
and "NCBI"
row names were re-validated against NCBI Taxonomy"short"
and "NCBI"
row names were re-validated against NCBI TaxonomycuratedMetagenomicData()
function now has a rownames
argument:
"long"
, the default character string derived from MetaPhlAn3"short"
, the NCBI Taxonomy species name from the CHOCOPhlAn database
"short"
row names are validated against NCBI Taxonomy with taxize
"NCBI"
, the NCBI Taxonomy ID from the CHOCOPhlAn database
"NCBI"
row names are validated against NCBI Taxonomy with taxize
rowData
becomes NCBI Taxonomy ID numbers instead of taxa namesdgTMatrix
to dgCMatrix
combined_metadata
object has been removedcuratedMetagenomicData()
function has been refactored for efficiency
SummarizedExperiment
/TreeSummarizedExperiment
objectsmergeData()
function has been refactored for accuracy and efficiencyreturnSamples()
function has been added for returns across studiessampleMetadata
object replaces the combined_metadata
objectcombined_metadata
object will be removed in the next releaseHMP_2012.pathcoverage.stool()
) have become defunct
curatedMetagenomicData()
function replaces all named accessors