Error in GroupCoverages

[EraslanBas]

Hi,

For some groups I am getting very small number of peaks. When I looked at these groups, I observed that there is something wrong with the names of the group coverage files of these samples (attached, STIM_10nM, STIM_100nM, STIM_10uM). Would you mind helping me with this issue?

Thanks in advance.

[rcorces]

You will need to provide more information. In particular a log file from addGroupCoverages() would be a good place to start

[EraslanBas]

Thank you for your reply Ryan! Attached is the log file of the whole run. Unlike other conditions STIM_10uM does not have _repX file names.

ArchR-addGroupCoverages-27da2b6033b2-Date-2023-03-19_Time-18-31-38.log

[rcorces]

I'm not 100% sure whats going on. Looking at your log file hasnt yielded a lot of insight. I would start by trying to identify why ArchR thinks that condition shouldnt get replicates. The easiest way to do this is to use returnGroups = TRUE and tweak some of the other input parameters. Minimally you could show me the output of returnGroups = TRUE and the number of cells per group (e.g. using table())

[EraslanBas]

Thank you Ryan! STIM_10uM and NOSTIM_10uM conditions are the only two conditions where each "Sample" (in the coldata) has more cells than the "minCells" parameter of addGroupCoverages(), which is set to 80. (attached are number of cells of the STIM_10uM and an example condition)

In the addGroupCoverages() function I saw the piece of code below, can this be the reason that these two conditions are named differently while generating the group coverages?

[rcorces]

Can you run the below code and send me the 4 RDS files it produces? I think I can help debug with that. You can send to [email protected]

#I based these values on your log file
ArchRProj <- #YOUR ARCHR PROJ HERE
groupBy <- "compoundDosage"
useLabels <- TRUE
sampleLabels <- "Sample"
minCells <- 80
maxCells <- 500
maxFragments <- 2.5e+07
minReplicates <- 2
maxReplicates <- 5
sampleRatio <- 0.8
kmerLength <- 6
threads <- 90
returnGroups <- FALSE
parallelParam <- NULL
force <- TRUE
verbose <- TRUE

#####################################################
#Groups 
#####################################################
cellNames <- rownames(getCellColData(ArchRProj))
groups <- getCellColData(ArchRProj, groupBy, drop = TRUE)
if(any(is.na(groups))){
    cellNames <- cellNames[!is.na(groups)]
    groups <- groups[!is.na(groups)]
}
uniqueGroups <- gtools::mixedsort(unique(groups))
tableGroups <- table(groups)[uniqueGroups]


x <- which(uniqueGroups == "STIM_10uM")

cellColData <- getCellColData(ArchRProj)

saveRDS(object = cellNames, file = "cellNames.RDS")
saveRDS(object = groups, file = "groups.RDS")
saveRDS(object = uniqueGroups, file = "uniqueGroups.RDS")
saveRDS(object = cellColData, file = "cellColData.RDS")