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@lwaldron
Created November 23, 2022 15:26
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identify cMD datasets producing error
suppressPackageStartupMessages(library(curatedMetagenomicData))
sampleMetadata[sampleMetadata$study_name == "FengQ_2015", ] |>
returnSamples("relative_abundance", rownames = "NCBI")
allstudies <- unique(sampleMetadata$study_name)
allres <- sapply(allstudies, function(study) {
message(study)
try(
suppressMessages(sampleMetadata[sampleMetadata$study_name == study,] |>
returnSamples("relative_abundance", rownames = "NCBI"))) |>
class()
})
names(allres)[allres == "try-error"]
BiocManager::version()
BiocManager::valid()
sessionInfo()
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