Marker file error "arker file error. Illegal character"

[Connor Finkbeiner]

I wanted to test out the Garnett automated notation so I created a markerfile and attempted to reload it onto the old data:

type_marker_test_res = top_markers(cds,

                                  group_cells_by="cluster",

                                  reference_cells=1000,

                                  cores=8)

# Require that markers have at least JS specificty score > 0.5 and

# be significant in the logistic test for identifying their cell type:

garnett_markers = type_marker_test_res %>%

    filter(marker_test_q_value < 0.01 & specificity >= 0.5) %>%

    group_by(cell_group) %>%

    top_n(5, marker_score)

# Exclude genes that are good markers for more than one cell type:

garnett_markers = garnett_markers %>% group_by(gene_short_name) %>%

    filter(n() == 1)

generate_garnett_marker_file(garnett_markers, file="~\marker_file.txt")

class <- train_cell_classifier(cds = cds,

                                  marker_file =

                                  "~\marker_file.txt",

                                  db=org.Mm.eg.db::org.Mm.eg.db, 

                                  num_unknown = 50,

                                  marker_file_gene_id_type = "SYMBOL",

                                  cores=8)

When running the last function I get the error:

'arker file error. Illegal character '

And the error:

Error in self$errorfunc(errtoken) : ' at or near line number 1x error '

Is there a way to get the illegal character? It looks like there is a bug in that error message and it is not being sliced properly.

Any debugging recommendations?

[Hannah Pliner]

I think this might be caused by the backwards slash in your file path. Can you try running it again with file="~/marker_file.txt"?

Hannah