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the great refactor #16

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merged 16 commits into from
Mar 12, 2024
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get tests passing again
d-callan committed Mar 7, 2024
commit a564e976ad48ca1e80ae6c83e7ba53600acf4b73
2 changes: 1 addition & 1 deletion R/method-differentialAbundance.R
Original file line number Diff line number Diff line change
@@ -103,7 +103,7 @@ setGeneric("deseq",
signature = c("data", "comparator")
)

setMethod("deseq", signature("microbiomeData::AbsoluteAbundanceData", "Comparator"), function(data, comparator, verbose = c(TRUE, FALSE)) {
setMethod("deseq", signature("AbsoluteAbundanceData", "Comparator"), function(data, comparator, verbose = c(TRUE, FALSE)) {
recordIdColumn <- data@recordIdColumn
ancestorIdColumns <- data@ancestorIdColumns
allIdColumns <- c(recordIdColumn, ancestorIdColumns)
2 changes: 1 addition & 1 deletion tests/testthat/test-correlation.R
Original file line number Diff line number Diff line change
@@ -290,7 +290,7 @@ test_that("correlation fails with improper inputs", {
)


data <- microbiomeComputations::AbsoluteAbundanceData(
data <- microbiomeData::AbsoluteAbundanceData(
data = counts,
sampleMetadata = sampleMetadata,
recordIdColumn = 'entity.SampleID')