Running infercna errors

[ConDem94]

Hi, I am trying to use infercna as an alternative to infercnv and copykat as I need a faster cnv caller for my large integrated dataset (200,000+ cells).

I installed your package using this code:

BiocManager::install("Homo.sapiens")
BiocManager::install("jpmam1/scalop") # Jared's awesome forked copy
BiocManager::install("jlaffy/infercna")

After following the vignette, and successfully running infercna, I am getting an error when I try to run cnaPlot:

m = useData(mgh125)
dim(m)
range(m)
lengths(refCells)

args(infercna)
cna = infercna(m = m, refCells = refCells, n = 5000, noise = 0.1, isLog = TRUE, verbose = FALSE)
cnaM = cna[, !colnames(cna) %in% unlist(refCells)]

args(cnaPlot)
obj = cnaPlot(cna = data.frame(cnaM),
              order.cells = F,
              subtitle = 'Copy-Number Aberrations in a patient with Glioblastoma')
names(obj)

Error: Error in `data_frame()`:
! `yintercept` must be a vector, not a <waiver> object.

Also, when I try to run findMalignant using this code:

Modes = findMalignant(cna, signal.threshold = .9, samples = 'MGH125')

Calculating cells' CNA correlations...
Error: 'split_by_sample_names' is not an exported object from 'namespace:scalop'

So there must be an issue with the scalop package? Has anyone resolved this?

Best wishes,
Constantinos

[Guanchen-Li]

findMalignant(cna = cna,samples = NULL)

Note, we jsut need to add this one: samples = NULL into the findMalignant function.