Hello,
I working on R package methylKit, while using obj=read.transcript.features("final.bed") Get an error message: Error in read.transcript.features("final.bed"): unused argument ("final.bed")
Can anyone guide how to solve this error?
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written
by
bruseq •
Please provide, as suggested in the comments, information about your system, including what version of the package you have installed. Looking at the current version in github, and as mentioned in the comments, the function read.transcript.features() has been deprecated. However, the replacement function, readTranscriptFeatures() cannot be found in the methylKit package, but in the Bioconductor package genomation. Since in your posted error message you didn't get the deprecation message (see below), I am guessing you have an earlier version of the package. Probably it is better that you have the latest release version installed.
#' @rdname genomation-deprecated
#' @aliases read.transcript.features
#' @export
read.transcript.features<-function(){
.Deprecated("genomation::readTranscriptFeatures")
message("Use functions in genomation package from Bioconductor\n",
"See vignette for examples.")}
Sir, I get this deprecated message when using below command > read.transcript.features function () { .Deprecated("genomation::readTranscriptFeatures") message("Use functions in genomation package from Bioconductor\n", "See vignette for examples.") } <environment: namespace:methylkit=""> I install genomation package also but same error occurs. Atlast it shows an unused argument error,
so please suggest me what next step i do.
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Not sure if this is the issue but read.transcript.features() is deprecated and replaced by readTransciptFeatures() according to the project news page.
Another possibility is that you have another function with the same name.
Thanks for reply But again this error occurs obj=readTranscriptFeatures("final.bed") Error: could not find function "readTranscriptFeatures"
Why this "unused argument" error occur. Please guide me if there is any other way to sort this error.
To get proper help say which version of R and packages attached. Use
sessionInfo()for this purpose.I m using > sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS and methylKit_1.0.0 version and Bioconductor boiCLite_package version 3.4
I am also having the same issue and the function is written below:
The error message is unused argument.
Please help me in moving forward by resolving the error.
Please open a new question and add a link to this top-level post. Do not add an answer unless you're answering the top level question.
Once you open the new question, use the
moderateoption to delete your answer here.The vignette says:
readTranscriptFeaturesreads a bed12 formatted file - so only one file, not two like you've used heresystem.file()is the function that has thepackage=argument, notreadTranscriptFeatures.Please read the manual/vignette before asking us to help you.