LEfSe for multiple samples
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6 weeks ago
willnotburn ▴ 40

I have 5 groups of samples, all with different abundances of various genes (KOs). Is there a LEfSe implementation that compares 5 groups at the same time?

R Bioconductor has a user-friendsly package lefser, but it only takes two groups at a time as input.

RNA-Seq metagenomics environmental genomics • 136 views
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You can use lefser for that propose. Have a look into the argument one.against.one : for multiclass tasks, sets whether testing is performed one-against-one (TRUE - more strict) or one-against-all (FALSE - less strict)

So if you have 5 groups: A,B,C,D and E, for the all-against-all feature has to be differential abundant between all the 5 groups (feature p is detected if its abundance is different in A vs B, A vs C, A vs D, B vs C...) . And for one against all: Feature p is detected if its abundance is different in A vs B, A vs C, A vs D but not necessary in A vs E for example)

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That would be exactly what I need! But I'm not seeing those arguments in lefser. Is there a development version? I installed mine off of Bioconductor, and it's Version: 1.0.0

lefser(
expr,
kruskal.threshold = 0.05,
wilcox.threshold = 0.05,
lda.threshold = 2,
groupCol = "GROUP",
blockCol = NULL,
assay = 1L,
trim.names = FALSE
)

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you can try this. Other option is to use Galaxy m that has a very good implemented interface to address this issue. Is less manipulative but is very straight forward

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Thank you! The lefse function in yingtools2 seems like a more mature implementation than a standalone lefser package.