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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Bug `get_DE_info` when option `findMarkers = TRUE` #19

Closed browaeysrobin closed 1 year ago

browaeysrobin commented 1 year ago

See issues #12 and #13 : bug in code of get_DE_info when option findMarkers = TRUE

browaeysrobin commented 1 year ago

No problem -- just be aware: if using findMarkers = TRUE, you need to provide a contrast_tbl as argument (this is now specified in the error message in the function in release version 2 -- currently on devel-branch, later main branch)

DE_info_FM = get_DE_info(sce, sample_id, group_id, celltype_id, batches, covariates, contrasts_oi, min_cells = 10, assay_oi_pb = "counts", fun_oi_pb = "sum", de_method_oi = "edgeR", findMarkers = TRUE, contrast_tbl = contrast_tbl, filterByExpr.min.count = 7, filterByExpr.min.total.count = 15, filterByExpr.large.n = 4, filterByExpr.min.prop = 0.7)