how to make custom feature matrices in archr object

[yingyuan830]

I'd like to add a new peak-by-cell matrix to the archr object for the next step marker peak analysis, but not very sure how to make it work, can anyone give some hints ? Thanks! BTW, for the peak-by-cell matrix, if I have got the merged peak bed file, what is a reasonable method to count if a peak range of one cell is in the merged peak range ?

[rcorces]

change your peak set to whatever you want using addPeakSet() and then re-run addPeakMatrix(). You can only have one peak matrix at a time.

[yingyuan830]

For the peak set, can I just give the chrome name and start-end information, but ignore other parts ? I am not very sure how this will influence the later analysis..

[yingyuan830]

There are some errors when I run addPeakMatrix() after I use addPeakSet() on my own peakset, can you please help me ? Thanks!

Warning message in mclapply(..., mc.cores = threads, mc.preschedule = preschedule):
“8 function calls resulted in an error”
Error in (function (..., threads = 1, preschedule = FALSE) :
Error Found Iteration 1 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 2 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 3 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 4 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 5 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 6 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 7 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 8 :
[1] "Error in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".addFeatureMatrix", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above>

Traceback:

1. addPeakMatrix(proj)
2. .batchlapply(args)
3. do.call(.safelapply, args)
4. (function (..., threads = 1, preschedule = FALSE)
   . {
   . if (tolower(.Platform$OS.type) == "windows") {
   . threads <- 1
   . }
   . if (threads > 1) {
   . .requirePackage("parallel", source = "cran")
   . o <- mclapply(..., mc.cores = threads, mc.preschedule = preschedule)
   . errorMsg <- list()
   . for (i in seq_along(o)) {
   . if (inherits(o[[i]], "try-error")) {
   . capOut <- utils::capture.output(o[[i]])
   . capOut <- capOut[!grepl("attr\(\,|try-error",
   . capOut)]
   . capOut <- head(capOut, 10)
   . capOut <- unlist(lapply(capOut, function(x) substr(x,
   . 1, 250)))
   . capOut <- paste0("\t", capOut)
   . errorMsg[[length(errorMsg) + 1]] <- paste0(c(paste0("Error Found Iteration ",
   . i, " : "), capOut), "\n")
   . }
   . }
   . if (length(errorMsg) != 0) {
   . errorMsg <- unlist(errorMsg)
   . errorMsg <- head(errorMsg, 50)
   . errorMsg[1] <- paste0("\n", errorMsg[1])
   . stop(errorMsg)
   . }
   . }
   . else {
   . o <- lapply(...)
   . }
   . o
   . })(ceiling = 4, binarize = FALSE, verbose = TRUE, threads = 8L,
   . force = TRUE, logFile = "ArchRLogs/ArchR-addPeakMatrix-2f155b0a58e2-Date-2022-09-13_Time-20-11-12.log",
   . ArrowFiles = c(FezF2 = "/ArchR/inte4/ArrowFiles/FezF2.arrow",
   . Unc5b = "/ArchR/inte4/ArrowFiles/Unc5b.arrow",
   . PlxnD1 = "/ArchR/inte4/ArrowFiles/PlxnD1.arrow",
   . PV = "/ArchR/inte4/ArrowFiles/PV.arrow",
   . vGlut1 = "/ArchR/inte4/ArrowFiles/vGlut1.arrow",
   . TLE4 = "/ArchR/inte4/ArrowFiles/TLE4.arrow",
   . Gad2 = "/ArchR/inte4/ArrowFiles/Gad2.arrow",
   . Cux1 = "/ArchR/inte4/ArrowFiles/Cux1.arrow"
   . ), allCells = c("PlxnD1#CTCAGAACATTACACG-1", "PlxnD1#CTTCTAATCCCTAAAG-1",
   . "PlxnD1#GTGGCGTCATGTATCG-1", "PlxnD1#CCGCATTAGTCCAGAG-1",
   . "PlxnD1#CTAGGATCAGGCTACC-1", "PlxnD1#ACCCAAATCCGCGATG-1",
   . "PlxnD1#TAGCTTTCAGAGAGAA-1", "PlxnD1#TCAAGGTCAGCGCGTT-1",
   . "PlxnD1#TTCGCGTGTCGATTAC-1", "PlxnD1#AAAGATGAGATGGCAC-1",
   . "PlxnD1#GCAGATTGTCATTGGT-1", "PlxnD1#AGCTATGTCTAAACGC-1",