Error after LSI $ operator is invalid for atomic vectors

[iremtelli1]

Hello,

I'm trying to use LSI Implementation as following:

archrproj2 <- addIterativeLSI(
  ArchRProj = archrproj2,
  useMatrix = "TileMatrix",
  name = "IterativeLSI",
  iterations = 2,
  clusterParams = list( #See Seurat::FindClusters
    resolution = c(0.5),
    sampleCells = 10000,
    maxClusters = 20,
    n.start = 10
  ),
  varFeatures = 25000,
  dimsToUse = 1:30,
  UMAPParams = list(n_neighbors = 120, min_dist = 0.25)
)

But I'm getting this error:

Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-2f7b63b15af43-Date-2021-06-27_Time-00-11-21.log
If there is an issue, please report to github with logFile!
2021-06-27 00:11:22 : Computing Total Accessibility Across All Features, 0.005 mins elapsed.
2021-06-27 00:11:25 : Computing Top Features, 0.057 mins elapsed.
###########
2021-06-27 00:11:26 : Running LSI (1 of 2) on Top Features, 0.064 mins elapsed.
###########
2021-06-27 00:11:26 : Sampling Cells (N = 10000) for Estimated LSI, 0.065 mins elapsed.
2021-06-27 00:11:26 : Creating Sampled Partial Matrix, 0.065 mins elapsed.
2021-06-27 00:11:39 : Computing Estimated LSI (projectAll = FALSE), 0.288 mins elapsed.
2021-06-27 00:12:33 : Identifying Clusters, 1.191 mins elapsed.

************************************************************
2021-06-27 00:12:34 : ERROR Found in FindNeighbors for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-2f7b63b15af43-Date-2021-06-27_Time-00-11-21.log

<simpleError in `[[<-`(`*tmp*`, "orig.ident", value = idents): [[<- defined for objects of type "S4" only for subclasses of environment>

************************************************************


************************************************************
2021-06-27 00:12:34 : ERROR Found in runClusters for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-2f7b63b15af43-Date-2021-06-27_Time-00-11-21.log

<simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************


************************************************************
2021-06-27 00:12:34 : ERROR Found in .LSICluster for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-2f7b63b15af43-Date-2021-06-27_Time-00-11-21.log

<simpleError in .logError(e, fn = "runClusters", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************

Error: $ operator is invalid for atomic vectors

I'm also getting the same error when I used the data in ArchR Tutorial:

library(ArchR)
inputFiles <- getTutorialData("Hematopoiesis")
inputFiles
addArchRGenome("hg19")
addArchRThreads(threads = 16) 
ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  filterTSS = 4, #Dont set this too high because you can always increase later
  filterFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)
doubScores <- addDoubletScores(
  input = ArrowFiles,
  k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
  knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
  LSIMethod = 1
)

Error:

ArchR logging to : ArchRLogs/ArchR-addDoubletScores-2f7b63f3e1cca-Date-2021-06-27_Time-00-49-22.log
If there is an issue, please report to github with logFile!
2021-06-27 00:49:22 : Batch Execution w/ safelapply!, 0 mins elapsed.
2021-06-27 00:49:22 : scATAC_BMMC_R1 (1 of 3) :  Computing Doublet Statistics, 0 mins elapsed.

************************************************************
2021-06-27 00:49:44 : ERROR Found in FindNeighbors for  
LogFile = ArchRLogs/ArchR-addDoubletScores-2f7b63f3e1cca-Date-2021-06-27_Time-00-49-22.log

<simpleError in `[[<-`(`*tmp*`, "orig.ident", value = idents): [[<- defined for objects of type "S4" only for subclasses of environment>

************************************************************


************************************************************
2021-06-27 00:49:44 : ERROR Found in runClusters for  
LogFile = ArchRLogs/ArchR-addDoubletScores-2f7b63f3e1cca-Date-2021-06-27_Time-00-49-22.log

<simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************


************************************************************
2021-06-27 00:49:44 : ERROR Found in .LSICluster for  
LogFile = ArchRLogs/ArchR-addDoubletScores-2f7b63f3e1cca-Date-2021-06-27_Time-00-49-22.log

<simpleError in .logError(e, fn = "runClusters", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************


************************************************************
2021-06-27 00:49:44 : ERROR Found in addIterativeLSI for scATAC_BMMC_R1 (1 of 3) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-2f7b63f3e1cca-Date-2021-06-27_Time-00-49-22.log

<simpleError: $ operator is invalid for atomic vectors>

************************************************************

Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile),  : 
  Exiting See Error Above

Could you please help me with that? Thank you very much in advance!

[rcorces]

This is a Seurat issue. I would try uninstalling and re-installing or updating all of your Seurat-related packages. Then start a clean R session (do no save and re-load the environment)

[iremtelli1]

It turns out I had an older Seurat version. Now everything is fine, thank you very much!