Several Errors when running scTyper without seurat pre processing

[LucieLamothe]

I am runing variations of

test.seurat=loadTestData()
# testseurat = load("~/Datas/deconv_pdac/GSE103322.seurat.reduced.rda")
pheno.fn=system.file("extdata/pheno_info_public.csv", package = "scTyper")
marker="Puram.2017.HNSCC.TME"
celltyped.seurat=scTyper(
                         seurat.object=test.seurat,
                         # seurat.object = peng_subset,
                         marker="Puram.2017.HNSCC.TME",
                         wd = getwd(),
                         output.name = "scTyper.output",
                         pheno.fn = pheno.fn,
                         qc = FALSE,
                         run.cellranger=FALSE,
                         norm.seurat=FALSE,
                         cell.typing.method="NTP",
                         level="cell",
                         run.inferCNV=TRUE,
                         proj.name = "scTyper",
                         gene.ref.gtf="/data/pubdata/ngs_ref/cellranger/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf",
                         # gene.ref.gtf="~/projects/pancreas_deconv_data/data_2024/input/02_input_gencode_v19_gene_pos.txt",
                         feature.to.test = "tissue.type",
                         cells.test_excluded=c("Epithelial_cell", "Unresolved_cell"),
                         cells.test_reference = "Normal",
                         malignant.cell.type="Epithelial_cell",
                         report.mode=TRUE,
                         # NTP.g.filter.method = "sd", # default is sd, error for now, "none" works until error
                         mc.cores = 1)

when NTP.g.filter.method is commented out , have the error

[[2024-06-06 17:25:48.328407]] Run NTP --------
Error in if (NTP.g.filter.method == "sd") { : 
  the condition has length > 1

same as #14 and #12

I had the same error when trying

gene.ref.gtf="/data/pubdata/ngs_ref/cellranger/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf"

and with another gtf file (provided by infercnv)

This error goes when I explicitly set the parameter : NTP.g.filter.method = "sd" but is replaced by

[[2024-06-06 17:36:27.890261]] Run NTP --------
Error in validObject(object = value) : 
  invalid class “Assay” object: slots in class definition but not in object: "assay.orig"
Error during wrapup: no slot of name "assay.orig" for this object of class "Assay"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

Which is also reported in #15

My interpretation is that it because of a faulty Seurat object because
> test.seurat@assays$RNA@assay.orig

returns

Error: no slot of name "assay.orig" for this object of class "Assay"
No suitable frames for recover()

So I tried and upload my personal seurat object and wich has a "assay.orig" slot (it is NULL but existant)

and I get

[[2024-06-06 17:48:22.126552]] Run NTP --------
Error in `$<-.data.frame`(`*tmp*`, "sd", value = c(HES4 = 1.30158055687105,  : 
  replacement has 3000 rows, data has 24005

same error as #6

I really don't know where this could be coming from.

I am a bit lost on what to do, could you help?