find_rank_bias {clustifyr} | R Documentation

## Find rank bias

### Description

Find rank bias

### Usage

    find_rank_bias(
      mat,
      metadata,
      type_col,
      ref_mat,
      query_genes = NULL,
      filter_out = TRUE,
      threshold = 0.33,
      expr_cut = 3000,
      consensus_cut = 1
    )

### Arguments

`mat` | original query expression matrix
`metadata` | metadata after calling types
`type_col` | column name in metadata that contains ids
`ref_mat` | reference expression matrix
`query_genes` | original vector of genes used to clustify
`filter_out` | whether to only report filtered results
`threshold` | diff threshold
`expr_cut` | consider all lower expressing genes as off
`consensus_cut` | filter out if lower han number of types show large diff

### Value

matrix of rank diff values

### Examples

    res <- clustify(
        input = pbmc_matrix_small,
        metadata = pbmc_meta,
        ref_mat = cbmc_ref,
        query_genes = pbmc_vargenes,
        cluster_col = "classified"
    )
    call1 <- cor_to_call(
        res,
        metadata = pbmc_meta,
        cluster_col = "classified",
        collapse_to_cluster = FALSE,
        threshold = 0.8
    )
    pbmc_meta2 <- call_to_metadata(
        call1,
        pbmc_meta,
        "classified"
    )
    find_rank_bias(
        pbmc_matrix_small,
        pbmc_meta2, "type",
        cbmc_ref,
        query_genes = pbmc_vargenes
    )

[Package clustifyr version 1.0.0 Index]