Question: LiftOver in R (error)
1
gravatar for viniciushs.z
5.0 years ago by
viniciushs.z20
Brazil
viniciushs.z20 wrote:

I am trying to use the LiftOver function in `rtracklayer` package but I am getting one error, this is my code:

    library(rtracklayer)
    library(gwascat)
    library(IRanges)
    
    chain <- import.chain("bosTau6.hg19.all.chain")
    
    df <- read.table(textConnection("chr  start  end
    chr5  58024309  58039917"), header =T)
    
    library(GenomicRanges)
    
    gr <- makeGRangesFromDataFrame(df, TRUE)
    
    humcon <- liftOver(gr, chain)

To download and extract the chain file into work folder I used:

    wget http://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/vsHg19/bosTau6.hg19.all.chain.gz
    gunzip gunzip bosTau6.hg19.all.chain.gz

The error follows:

    Warning message:
    'mseqapply' is deprecated.
    Use 'as(mapply(FUN, ...), 'List')' instead.
    See help("Deprecated")

Some ideas why it is not working? Thank you!

liftover bioconductor R genome • 3.0k views
ADD COMMENTlink modified 5.0 years ago by Sean Davis25k • written 5.0 years ago by viniciushs.z20
2
gravatar for Sean Davis
5.0 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Your code appears to have worked just fine.  What you are seeing is a "Warning".  Warnings are usually not critical (but need to be evaluated on a case-by-case basis).  In this case, I suspect that your liftOver worked just fine and that you can ignore the Warning.  

For future reference, in addition to example code, include the output of sessionInfo() when posting about R code problems.

ADD COMMENTlink written 5.0 years ago by Sean Davis25k
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