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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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The isoformCountMatrix contains character/factor column(s) (other than the isoform_id column) #125

Closed BennyMos closed 1 year ago

BennyMos commented 2 years ago

Hi I'm trying to run the importRdata command and am met with the above error. However when I check the data columns they all appear to be correct (numeric): 


> str(kallisto_Cyto$abundance)
'data.frame':   65195 obs. of  5 variables:
 $ isoform_id        : chr  "ENSMUST00000130201.7::chr1:4773205-4785710(-)" "ENSMUST00000156816.6::chr1:4773210-4785739(-)" "MSTRG.1.3::chr1:4773242-4785692(-)" "MSTRG.1.4::chr1:4773263-4785692(-)" ...
 $ cyto_ctlf_rep1.gtf: num  5.28 0.466 0 0 0 ...
 $ cyto_ctlf_rep2.gtf: num  4.2729 0.0144 0 0 0 ...
 $ cyto_lpsf_rep1.gtf: num  0.013 2.819 0 0 0 ...
 $ cyto_lpsf_rep2.gtf: num  0.013 2.819 0 0 0 ...
> str(kallisto_Cyto$counts)
'data.frame':   65195 obs. of  5 variables:
 $ isoform_id        : chr  "ENSMUST00000130201.7::chr1:4773205-4785710(-)" "ENSMUST00000156816.6::chr1:4773210-4785739(-)" "MSTRG.1.3::chr1:4773242-4785692(-)" "MSTRG.1.4::chr1:4773263-4785692(-)" ...
 $ cyto_ctlf_rep1.gtf: num  111.62 9.86 0 0 0 ...
 $ cyto_ctlf_rep2.gtf: num  60.079 0.202 0 0 0 ...
 $ cyto_lpsf_rep1.gtf: num  0.284 61.569 0 0 0 ...
 $ cyto_lpsf_rep2.gtf: num  0.284 61.569 0 0 0 ...
> str(kallisto_Cyto$length)
'data.frame':   65195 obs. of  5 variables:
 $ isoform_id        : chr  "ENSMUST00000130201.7::chr1:4773205-4785710(-)" "ENSMUST00000156816.6::chr1:4773210-4785739(-)" "MSTRG.1.3::chr1:4773242-4785692(-)" "MSTRG.1.4::chr1:4773263-4785692(-)" ...
 $ cyto_ctlf_rep1.gtf: num  12202 12226 12147 12126 12126 ...
 $ cyto_ctlf_rep2.gtf: num  12217 12241 12162 12141 12141 ...
 $ cyto_lpsf_rep1.gtf: num  12191 12215 12136 12115 12115 ...
 $ cyto_lpsf_rep2.gtf: num  12191 12215 12136 12115 12115 ...

Here is my full list of commands:

library(IsoformSwitchAnalyzeR)

kallisto_Cyto = importIsoformExpression(parentDir = "/Users/bennymosqueira/Downloads/Research lab/Brooks:Carpenter lab/Data_Test/",
                        showProgress = T)

myDesign <- data.frame(
  sampleID = colnames(kallisto_Cyto$abundance)[-1],
  condition = c("ctlf", "ctlf", "lpsf", "lpsf")
)

switchList = importRdata(kallisto_Cyto,
                         designMatrix = myDesign,
                         isoformExonAnnoation = "/Users/bennymosqueira/Downloads/Research lab/Brooks:Carpenter lab
                         /frac-seq_transcripts/merged_fracseq_transcripts.gtf")
kvittingseerup commented 2 years ago

I think you migth be suplying the entire list list to the isoformCountMatrix instead of the count matrix?

kvittingseerup commented 1 year ago

Closing due to no activity. If you respond I will open it again :)