Question

error in champ.SVD

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Entering edit mode

Giulia • 0

@fbbebaac

Last seen 19 months ago

Italy

Hello, when I run champ.SVD function I always obtain this kind of error, wthat is the problem?

Thank you!

Code should be placed in three backticks as shown below

library("ChAMP")
myLoad<-champ.load(directory="C:/Users/andre/methylation_CLL1", arraytype="EPIC")
champ.QC()
myNorm <- champ.norm(beta=myLoad$beta,arraytype="EPIC",cores=5)
QC.GUI(beta=myNorm,arraytype="EPIC")
champ.SVD(beta=myNorm,pd=myLoad$pd)

#> champ.SVD(beta=myNorm,pd=myLoad$pd)
[===========================]
[<<<<< ChAMP.SVD START >>>>>]
-----------------------------
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .

Error in if (class(beta) == "data.frame") { : 
  the condition has length > 1

svd methylation champ • 1.0k views

ADD COMMENT • link updated 19 months ago by shepherl 4.1k • written 19 months ago by Giulia • 0

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Entering edit mode

It is an ERROR in the champ code and will have to be fixed by the ChAMP maintainers. R introduced length > 1 conditional checks. If the results of class(beta) has multiple values from say extending a class than it will throw an error because the if statement will have a vector instead of a single value

ADD REPLY • link 19 months ago shepherl 4.1k

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Entering edit mode

dummy example:

> library(tibble)
> x = tibble()
> class(x)
[1] "tbl_df"     "tbl"        "data.frame"
> class(x) == "data.frame"
[1] FALSE FALSE  TRUE
> if(class(x) == "data.frame") { message("something")}
Error in if (class(x) == "data.frame") { : the condition has length > 1

They need to change the == likely to is() or surround in an any

> if(is(x,"data.frame")) { message("something")}
something

ADD REPLY • link 19 months ago shepherl 4.1k