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Convert a marker table to the ScInfeR format

Source: R/scrna-markers.R
markers_to_scinfer_df.Rd

A data.frame with celltype, marker and weight columns, the ct_marker_df that ScInfeR::predict_celltype_scRNA_seurat() takes.

Usage

markers_to_scinfer_df(df, tissue = NULL, cancer = NULL, species = NULL)

Arguments

df

A canonical marker table.

tissue

The tissue to filter by. If NULL, no filtering is done.

cancer

The cancer to filter by. If NULL, no filtering is done.

species

The species to filter by. If NULL, no filtering is done.

Value

A data.frame with celltype, marker and weight columns.

Details

Only positive markers are kept: ScInfeR has no direction, so a negative-direction marker would be counted as a marker of the cell type. The tool accepts per-marker weights but the universal marker table does not have to carry them: without a weight column every marker gets weight 1 (ScInfeR's own database weights each marker).