Question

"genomdat must be numeric"error in DNAcopy Package (Solved)

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jinxinhao1988 • 0

@jinxinhao1988-14864

Last seen 6.7 years ago

Hi,

I am using Varscan2 to call CNV in tumor-normal samples. After the first two steps, an output.copynumber file and copynumber.called file have been generated.

Then I followed the protocol to use the DNAcopy package to do the CBS segmentation,

My command line is as follows:

library(DNAcopy)

cn<-read.table("output.copynumber",header=F)

CNA.object <-CNA( genomdat = cn[,6], chrom = cn[,1], maploc = cn[,2], data.type = 'logratio')

But I got the error :

Error in CNA(genomdat = cn[, 6], chrom = cn[, 1], maploc = cn[, 2], data.type = "logratio") :
genomdat must be numeric

But the data in the coloum 6 of "output.copynumber" are all decimal numbers, so I am confused why I got this error?

Could anybody gave me some suggestions?

Thank you for your time.

DNAcopy Varscan • 1.9k views

ADD COMMENT • link updated 4.0 years ago by El • 0 • written 6.8 years ago by jinxinhao1988 • 0

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I was running the following command :

library(DNAcopy)

read.table <- function(file=x,header=FALSE,use.value.labels=TRUE,to.data.frame=TRUE,sep=",", widths=rep(1,36),f=NULL, filetype=tableau,...)

cn <- read.table(correct_copy), header=F)

CNA.object <-CNA( genomdat = as.numeric(cn[,36]), chrom = as.numeric(cn[,36]), maploc = as.numeric(cn[,36]), data.type = 'logratio',sampleid = "E47") ## as.numeric(cn[,36])

and I get rror: unexpected ',' in: " widths=rep(1,36),f=NULL, filetype=tableau,...) cn <- read.table(correct_copy),"

ADD REPLY • link 4.0 years ago El • 0

Kevin Blighe · Answer 1 · 2018-02-05

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Entering edit mode

jinxinhao1988 • 0

@jinxinhao1988-14864

Last seen 6.7 years ago

Hi,

After I change the "genomdat = cn[,6]" into "genomdat = as.numeric(cn[,6])" and "maploc = cn[,2]" into "maploc = as.numeric(cn[,2])". The problem has been solved.

Thank you.

ADD COMMENT • link updated 4.0 years ago by Kevin Blighe ★ 4.0k • written 6.8 years ago by jinxinhao1988 • 0

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please, I have a question, I didn't get over a type of error that's need a genomdat be numeric, the genomdat must be a date frame ....., I'm using the output of HMMcopy " correctreadcount , but didn't work the command line is

genomdat <- sample(correct_copy)

genomdat<- as.data.frame(genomdat)

CNA.object <- CNA(cbind(genomdat$genomdat.E47), genomdat$Chromosome, genomdat$Position, data.type="logratio",sampleid=c("cE47")) could any body had some solutions

ADD REPLY • link 4.0 years ago El • 0