Error in SCDC_prop() - Githubissues

Hi I am running SCDC for deconvolving 200 bulk samples. My current data looks like this : single cell data : ~10,000 genes and ~2500 unique cell IDs and their corresponding cell types in the metadata. Also the single cell data is multi subject and the sample names are given under the subjectname column in the metadata. bulk data : ~10000 genes and 200 individuals.

I get the following error when I run SCDC_prop():

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': NAs are not allowed in subscripted assignments 
8.h(simpleError(msg, call)) 
7..handleSimpleError(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)), "NAs are not allowed in subscripted assignments", 
    base::quote(y[y < q15] <- q15[y < q15])) 
6.FUN(newX[, i], ...) 
5.apply(var.adj, 1, function(y) {
    y[y < q15] <- q15[y < q15]
    y[y > q85] <- q85[y > q85]
    return(y) ... 
4.t(apply(var.adj, 1, function(y) {
    y[y < q15] <- q15[y < q15]
    y[y > q85] <- q85[y > q85]
    return(y) ... 
3.SCDC_basis(x = sc.eset, ct.sub = ct.sub, ct.varname = ct.varname, 
    sample = sample, ct.cell.size = ct.cell.size) 
2.SCDC::SCDC_prop(bulk.eset = T.eset, sc.eset = C.eset, ct.varname = "cellType", 
    sample = "SubjectName", ct.sub = unique(as.character(phenoDataC$cellType)), 
    iter.max = 200) at helper_functions.R#677
1.t(SCDC::SCDC_prop(bulk.eset = T.eset, sc.eset = C.eset, ct.varname = "cellType", 
    sample = "SubjectName", ct.sub = unique(as.character(phenoDataC$cellType)), 
    iter.max = 200)$prop.est.mvw) at helper_functions.R#677

let me know how I can fix this . Thanks , RK

meichendong / SCDC

Error in SCDC_prop() #18