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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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error in addGeneExpressionMatrix in ArchR(realease-1.0) #350

Closed RyanYip-Kat closed 3 years ago

RyanYip-Kat commented 4 years ago

I got the error : unable to find an inherited method for function ‘seqnames’ for signature ‘"SummarizedExperiment"’

when I run addGeneExpressionMatrix .It is a bug in these packages

rcorces commented 4 years ago

Thanks for posting. We would need more information to help you troubleshoot this. At first glance, this does not look like a problem with ArchR but rather a problem with how you are using ArchR. Please provide the code that you used to generate the error and the corresponding log file. Without this information, we are not able to respond.

RyanYip-Kat commented 4 years ago

I run the pipeline with your code provived in the pbmc.10k tutorial.And I just got this error in addGeneExpressionMatrix in ArchR. And I checked the seRNA with seqnames(seRNA),actually,the error produced in here

rcorces commented 4 years ago

Please provide the code that you used to generate the error and the corresponding log file. Without this information, we are not able to respond.

RyanYip-Kat commented 4 years ago

ArchR-addGeneExpressionMatrix-bba07e23015b-Date-2020-10-18_Time-01-07-24.log This is my log file

rcorces commented 4 years ago

Please provide the code that you used to generate the error

jgranja24 commented 4 years ago

My guess is that you used 2 samples and this bug was fixed last night. Please reinstall the release version and I think this will clean up your problem!

Best

Jeff

jgranja24 commented 4 years ago

If you want to continue my guess is seRNA for you is a list right now so you could do to fix it...

seRNA <- Reduce("cbind", seRNA)

The code change last night fixed this

  featureMats <- tryCatch({
    Reduce("cbind", featureMats)
  }, error = function(e){
    message("Error in combining individual feature matrices! Returning as a list of individual feature matrices!")
    featureMats
  })
RyanYip-Kat commented 4 years ago

ArrowFiles=c("/scATAC/ArchR/20201010/ArchR_results/CEpi_Mouse2/Save-ProjHeme/ArrowFiles/MSCE-24h-1-ATAC.arrow","/scATAC/ArchR/20201010/ArchR_results/CEpi_Mouse2/Save-ProjHeme/ArrowFiles/MSCE-24h-2-ATAC.arrow")

H5CountsFiles=c("/Data/MSCE-24h-1-RNA/outs/filtered_feature_bc_matrix.h5","/Data/MSCE-24h-2-RNA/outs/filtered_feature_bc_matrix.h5")

Samples=c("MSCE-24h-1-ATAC","MSCE-24h-2-ATAC")

seRNA <- import10xFeatureMatrix( input = H5CountsFiles, names = Samples )

seRNA <- Reduce("cbind", seRNA)

print("### Create ArchRProject") proj <- ArchRProject( ArrowFiles = ArrowFiles, copyArrows = TRUE #This is recommened so that if you modify the Arrow files you have an original copy for later usage. )

proj=addGeneExpressionMatrix(input = proj, seRNA = seRNA, force = TRUE)

I changed the code according to your suggestion.And I reinstalled the ArchR 1.0.0,when I run seRNA <- Reduce("cbind", seRNA) ,I got a new error : Error in FUN(X[[i]], ...) : column(s) 'id' in ‘mcols’ are duplicated and the data do not match,this mean SummarizedExperiment objects can not be cbinded. And even I just use one sample to use addGeneExpressionMatrix function,I still got the same error ： Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'which': error in evaluating the argument 'x' in selecting a method for function 'match': unable to find an inherited method for function ‘seqnames’ for signature ‘"SummarizedExperiment"’

RyanYip-Kat commented 4 years ago

my seRNA ：

class: SummarizedExperiment dim: 31017 15489 metadata(0): assays(1): counts rownames(31017): Xkr4 Gm1992 ... Vmn2r122 CAAA01147332.1 rowData names(4): feature_type genome id name colnames(15489): MSCE-24h-1-ATAC#AAACCCAAGAGCTGAC-1 MSCE-24h-1-ATAC#AAACCCAAGCGCCTAC-1 ... MSCE-24h-1-ATAC#TTTGTTGTCCAGGACC-1 MSCE-24h-1-ATAC#TTTGTTGTCGCTTACC-1 colData names(0):

my proj ： class: ArchRProject outputDirectory: /scATAC/ArchR/src-developing/ArchROutput samples(1): MSCE-24h-1-ATAC sampleColData names(1): ArrowFiles cellColData names(15): Sample TSSEnrichment ... DoubletEnrichment BlacklistRatio numberOfCells(1): 14372 medianTSS(1): 8.1205 medianFrags(1): 7048.5

jgranja24 commented 4 years ago

The seRNA from your logfile is not a Summarized Experiment like you show here

addGeneExpressionMatrix Input-Parameters$seRNA: nRows = 1, nCols = 2
     [,1] [,2]
[1,] ?    ?

Can you retry with a Summarized Experiment and if the bug occurs post the associated log file!

Thanks

Jeff

RyanYip-Kat commented 4 years ago

ArchR-addGeneExpressionMatrix-243fc559820-Date-2020-10-19_Time-08-20-06.log This is the new log file

jgranja24 commented 4 years ago

So the error is no overlap. I need to throw an error here

2020-10-19 08:20:07 : Overlap w/ scATAC = 0
2020-10-19 08:20:07 : Overlap Per Sample w/ scATAC : MSCE-24h-1-ATAC=6

Can you show

sum(proj$cellNames %in% colnames(seRNA))

and

sum(colnames(seRNA) %in% proj$cellNames)

and

head(proj$cellNames)

Thanks!

RyanYip-Kat commented 4 years ago

![Uploading 1603095035(1).jpg…]()

jgranja24 commented 4 years ago

Hi @RyanYip-Kat,

Your image isnt fully uploaded. Can you repost it?

Best

Jeff

jgranja24 commented 3 years ago

Hi @RyanYip-Kat,

Your image isnt fully uploaded you have to wait time when you paste images. Can you repost it? If not I will assume your issue has been resolved.

Best

Jeff

rcorces commented 3 years ago

Closing due to inactivity. Feel free to post to this thread if the problem can be reproduced with the latest version of ArchR and we will re-open the issue.