Hi,
I am using the RIPSeeker bioconductor package in R to run some RIPSeq analysis. I was able to successfully run the main ripseek() command and got my output files etc.
I am now trying to view the files using the viewRIP() function but keep running into errors. Any insight would be appreciated.
The output of ripSeek() function is annotated files (.bed/gff3 and txt) plus the SeekOutput.RData file.
setwd("/.../output")
getwd()
extdata.dir <- getwd()
outputfiles <- list.files(extdata.dir,".RData", recursive = TRUE, full.names = TRUE)
load(outputfiles, verbose = TRUE)
prints:
mainSeekOutputRIP, RIPGRList, mainSeekOutputCTL , annotatedRIPGR
To extract files within each I run:
alignGalFiltered <- elementMetadata(mainSeekOutputRIP$alignGalFiltered)
alignGalFiltered2 <- elementMetadata(mainSeekOutputCTL$alignGalFiltered)
viewRIP(RIPGRList@elementMetadata@listData, alignGalFiltered, alignGalFiltered2, scoreType = "eFDR", cutoffLine = .001)
PRINTS:
Error in (function (classes, fdef, mtable): unable to find an inherited method for function 'values' for signature '"list"'
OR
viewRIP(RIPGRList@elementMetadata, alignGalFiltered, alignGalFiltered2, scoreType = "eFDR", cutoffLine = .001)
PRINTS:
Error in log10(values(seekedRIP)[, scoreType]) : non-numeric argument to mathematical function
The viewRIP() first line in the code is:
{values(seekedRIP)[,scoreType] <- -log10(values(seekedRIP)[,scoreType])
I have tried multiple ways of running the function but it seems it is a problem with extracting the "column" from the S4 object/GRangesList. I have tried multiple ways to extract slots etc or trying to turn the S4 vector into a data frame but with no success, maybe I am doing it wrong. The column "eFDR" is located at
RIPGRList@elementMetadata@listData$eFDR (
also gives the error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'values' for signature '"numeric"')
Thanks for any help.
