Error in getHighExpGene: invalid or not-yet-implemented 'Matrix' subsetting

[mossnicholas]

I get the following error running RunMLnet, using the documented input formats:

head(control_meta_MLnet)
barcode assigned_cell_type
AAACCCAAGACAAGCC_1 AAACCCAAGACAAGCC_1 Fibroblast (1)
AAACCCAAGACTGTTC_1 AAACCCAAGACTGTTC_1 Fibroblast (1)
AAACCCAAGATACTGA_1 AAACCCAAGATACTGA_1 Macrophage, Dendritic (1)
AAACCCAAGCGTCGAA_1 AAACCCAAGCGTCGAA_1 Keratinocyte (1)
AAACCCAAGGAAGTGA_1 AAACCCAAGGAAGTGA_1 Macrophage, Dendritic (1)
AAACCCAAGGTCATCT_1 AAACCCAAGGTCATCT_1 Keratinocyte (1)

head(control_assay)

6 x 68364 sparse Matrix of class "dgCMatrix"
[[ suppressing 34 column names ‘AAACCCAAGACAAGCC_1’, ‘AAACCCAAGACTGTTC_1’, ‘AAACCCAAGATACTGA_1’ ... ]]

TMEM35A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
RIPPLY1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ZNF157 . . . . 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ARX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
PLS3 . . . . . . 1 . 1 . . 2 . . . 3 . . . . . . . . . . 2 . . . . 1 1 .
EMD . . 2 2 . . . . . 2 1 . . . 1 2 . . . . . . . 1 2 . . 1 1 3 3 1 . .

TMEM35A ......
RIPPLY1 ......
ZNF157 ......
ARX ......
PLS3 ......
EMD ......

.....suppressing 68330 columns in show(); maybe adjust 'options(max.print= *, width = *)'
..............................

netList <- RunMLnet(GCMat = control_assay,
BarCluFile = "control_meta_MLnet.txt",
RecClu = "Keratinocyte",
LigClu = "T-cell"
)
[1] "check table cell:"
[1] 0 2
[1] "Rec Cluster:"
[1] "Keratinocyte"
[1] "Lig Cluster:"
[1] "T-cell"
[1] "p val:"
[1] 0.05
[1] "logfc:"
[1] 0.15
[1] "get High Exp Gene in Keratinocyte"
[1] "Keratinocyte:0"
[1] "gene:15898"
Error in data.use[, cells, drop = F] :
invalid or not-yet-implemented 'Matrix' subsetting