Replicate the signac gene activity score model

[myylee]

Hi, thanks for the great package.

I want to implement the same gene activity score model used in the Signac package, which is the sum of reads mapped to gene body + 2kb upstream.

I'm not sure if the parameters I have for the addGeneScoreMatrix are correct, anyone suggestion/comment will help!

proj <- addGeneScoreMatrix(proj,geneModel="1",
matrixName="GeneScoreMatrix_signac",
geneUpstream = 2000,
logFile = createLogFile("addGeneScoreMatrix_signac"))

[rcorces]

If you are looking to exactly replicate Signac, I dont think I can help you with that since I do not know anything more about Signac's current gene score model than what you put in your question. i.e. I dont know if Signac uses gene boundaries, scale factors, etc. Here is my best attempt:

addGeneScoreMatrix(
  input = proj,
  geneModel = "1",
  matrixName = "GeneScoreMatrix_signac",
  extendUpstream = c(0, 0),
  extendDownstream = c(0, 0),
  geneUpstream = 2000,
  geneDownstream = 0,
  useGeneBoundaries = FALSE,
  useTSS = FALSE,
  tileSize = 500,
  ceiling = 4,
  geneScaleFactor = 5,
  scaleTo = 10000,
  excludeChr = c("chrY", "chrM"),
  blacklist = getBlacklist(input),
  threads = getArchRThreads(),
  parallelParam = NULL,
  subThreading = TRUE,
  force = FALSE,
  logFile = createLogFile("addGeneScoreMatrix")
)

[chen-zhan]

Hi, thanks for your kindness!

I meet an error "<simpleError in .logError(e, fn = ".addGeneScoreMat TmpGS", info = sampleName, errorList = errorList, logFile = logFile): Exiting See Error Above>". So I try to run proj = addGeneScoreMatrix(proj,c=FALSE).

And I read introduction of "addGeneScoreMatrix". But I am double about the result of switch addGeneScoreMatrix from TRUE to FALSE.
It will influent my data badly?