LiftOver in R (error)

Question

[viniciushs.z]

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!

Answer 1

[Sean Davis]

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.