Problem with dplyr during addORFfromGTF

[Caleb]

I am trying to analyze annotated and novel isoforms, but keep running into problems with the addORFfromGTF step. Mapping was done with HISAT2 and the transcript assembly, merge, and quantification were all done with StringTie. I am using version 1.20.0 of IsoformSwitchAnalyzeR and version 4.2.2. Here is my code up until I get the error:

library(IsoformSwitchAnalyzeR)
library(dplyr)
setwd("C:/Users/Caleb/OneDrive - The Ohio State University/BioinfoData/IsoformSwitch/ENCODE_EFTUD2")

#Import datasets
EFTUD2quant = importIsoformExpression(parentDir = "C:/Users/Caleb/OneDrive - The Ohio State University/BioinfoData/IsoformSwitch/ENCODE_EFTUD2",
                                      addIsofomIdAsColumn = TRUE, showProgress = TRUE, readLength = 100) #reads the t_data.ctab file in each sub directory
names(EFTUD2quant)

#Generate the list of isoform switches
myDesign = data.frame(sampleID = c("SRR4421357","SRR4421358","SRR4422087","SRR4422088"),
                      condition = c("KD","KD","WT","WT"))
SwitchList = importRdata(isoformCountMatrix = EFTUD2quant$counts,
                         isoformRepExpression = EFTUD2quant$abundance,
                         designMatrix = myDesign,
                         isoformExonAnnoation = "C:/Users/Caleb/OneDrive - The Ohio State University/BioinfoData/IsoformSwitch/ENCODE_EFTUD2/EFTUD2_stringtie_merged.gtf",
                         showProgress = TRUE)
SwitchList_filt = preFilter(SwitchList,
                            geneExpressionCutoff = 1, #Cut off genes with less than 1 TPM
                            isoformExpressionCutoff = 0, #removes unused isoforms
                            removeSingleIsoformGenes = TRUE, #removes genes with a single isoform
                            ) #The filtering removed 71938 ( 44.11% of ) transcripts. There is now 91136 isoforms left

#Perform switch test (will take a while)
AnalyzedSwitch = isoformSwitchTestDEXSeq(switchAnalyzeRlist = SwitchList_filt, #Uses DEXseq to analyze the isoform switches
                                         alpha = 0.05, #The FDR p-value has to be less than this
                                         dIFcutoff = 0.1, #THere must be at least a 10% change for the isoforms to be considered
                                         reduceToSwitchingGenes = TRUE, #This only keeps genes with one isoform significantly differently used, makes it run faster
                                         showProgress = TRUE)

#Identify ORFs
SwitchAndORF = addORFfromGTF(AnalyzedSwitch,
                             pathToGTF = "C:/Users/Caleb/OneDrive - The Ohio State University/BioinfoData/IsoformSwitch/Homo_sapiens.GRCh38.108.gtf")

When I run that line it appears to load the GTF fine but I get the following error: 

Step 1 of 2: importing GTF (this may take a while)... 

Error in `dplyr::full_join()`: 

! `...` must be empty. 

✖ Problematic argument: 

• all = TRUE

When I run rlang::last_error() I get the following:

<error/rlib_error_dots_nonempty> Error in `dplyr::full_join()`: ! `...` must be empty. ✖ Problematic argument: • all = TRUE

--- 

Backtrace: 

1. IsoformSwitchAnalyzeR::addORFfromGTF(AnalyzedSwitch, pathToGTF = "C:/Users/Caleb/OneDrive - The Ohio State University/BioinfoData/IsoformSwitch/Homo_sapiens.GRCh38.108.gtf") 

4. IsoformSwitchAnalyzeR::importGTF(...) 

6. dplyr:::full_join.data.frame(...)

I'm not sure what is going wrong here. I've tried updating all the packages.

[Caleb]

I tried running the example of addORFfromGTF from the help page and I get the same error with dplyr

[Caleb]

I found the update you posted on github and the new version seems to have fixed the problem. 

[Tainã Cardoso]

Hi,

I have the same problem.

Could you tell me which version you update?

I have already tried to update with the information available by
- https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html
- https://github.com/kvittingseerup/IsoformSwitchAnalyzeR

but without success...

[Kristoffer Vitting-Seerup]

You need IsoformSwitchAnalyzeR >= 2.1.0 which you can get from github.

Remember to restart R after updating

[C Doig]

Hi. I'm having trouble finding IsoformSwitchAnalyserR V 2.1.0. I cant find it on github nor Bioconductor. I'd be very thankful if you can post a link to take me to the .tar.gz

[Kristoffer Vitting-Seerup]

Just follow the installation instructions on github :-)