LEfSe for multiple samples
0
0
Entering edit mode
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
ADD COMMENT
1
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

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
)
ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2353 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6