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lefser on pathway abundances using ZellerG_2014 from cMD
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suppressPackageStartupMessages({ | |
library(lefser) | |
library(curatedMetagenomicData) | |
}) | |
zeller <- | |
curatedMetagenomicData("ZellerG_2014.pathway_abundance", | |
counts = TRUE, | |
dryrun = FALSE)[[1]] | |
zeller <- zeller[, zeller$study_condition != "adenoma"] | |
zeller <- relativeAb(zeller) | |
lefse_results1 <- | |
lefser( | |
zeller, | |
groupCol = "study_condition", | |
kruskal.threshold = 0.05, | |
lda.threshold = 2 | |
) | |
head(lefse_results1) | |
lefse_results2 <- | |
lefser( | |
zeller, | |
groupCol = "study_condition", | |
kruskal.threshold = 1e-6, | |
lda.threshold = 2 | |
) | |
head(lefse_results2) | |
lefse_results3 <- | |
lefser( | |
zeller, | |
groupCol = "study_condition", | |
kruskal.threshold = 0.05, | |
lda.threshold = 2000 | |
head(lefse_results3) |
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