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lwaldron/testlefsercounts

Created July 3, 2023 09:40
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Compare lefser output with relab and counts
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testlefsercounts
suppressPackageStartupMessages(library(curatedMetagenomicData))
zeller <- curatedMetagenomicData::curatedMetagenomicData("Zeller.+relative_abundance", counts = FALSE, dryrun = FALSE)[[1]]
zellercounts <- curatedMetagenomicData::curatedMetagenomicData("Zeller.+relative_abundance", counts = TRUE, dryrun = FALSE)[[1]]
zeller <- zeller[, zeller$study_condition != "adenoma"]
zellercounts <- zellercounts[, zellercounts$study_condition != "adenoma"]
suppressPackageStartupMessages(library(lefser))
res_group <- lefser(zeller, groupCol = "study_condition")
res_group_counts <- lefser(zellercounts, groupCol = "study_condition")
head(res_group)
head(res_group_counts)
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