pos_neg_select {clustifyr} | R Documentation

## adapt clustify to tweak score for pos and neg markers

### Description

adapt clustify to tweak score for pos and neg markers

### Usage

    pos_neg_select(
      input,
      ref_mat,
      metadata,
      cluster_col = "cluster",
      cutoff_n = 0,
      cutoff_score = 0.5
    )

### Arguments

`input` | single-cell expression matrix
`ref_mat` | reference expression matrix with positive and negative markers(set expression at 0)
`metadata` | cell cluster assignments, supplied as a vector or data.frame. If data.frame is supplied then `cluster_col` needs to be set. Not required if running correlation per cell.
`cluster_col` | column in metadata that contains cluster ids per cell. Will default to first column of metadata if not supplied. Not required if running correlation per cell.
`cutoff_n` | expression cutoff where genes ranked below n are considered non-expressing
`cutoff_score` | positive score lower than this cutoff will be considered as 0 to not influence scores

### Value

matrix of numeric values, clusters from input as row names, cell types from ref_mat as column names

### Examples

    pn_ref <- data.frame(
        "Myeloid" = c(1, 0.01, 0),
        row.names = c("CD74", "clustifyr0", "CD79A")
    )

    pos_neg_select(
        input = pbmc_matrix_small,
        ref_mat = pn_ref,
        metadata = pbmc_meta,
        cluster_col = "classified",
        cutoff_score = 0.8
    )

[Package clustifyr version 1.4.0 Index]