compare_lists {clustifyr} | R Documentation

## Calculate adjusted p-values for hypergeometric test of gene lists or jaccard index

### Description

Calculate adjusted p-values for hypergeometric test of gene lists or jaccard index

### Usage

    compare_lists(
      bin_mat,
      marker_mat,
      n = 30000,
      metric = "hyper",
      output_high = TRUE,
      details_out = FALSE
    )

### Arguments

`bin_mat` | binarized single-cell expression matrix, feed in by_cluster mat, if desired
`marker_mat` | matrix or dataframe of candidate genes for each cluster
`n` | number of genes in the genome
`metric` | adjusted p-value for hypergeometric test, or jaccard index
`output_high` | if true (by default to fit with rest of package), -log10 transform p-value
`details_out` | whether to also output shared gene list from jaccard

### Value

matrix of numeric values, clusters from expr_mat as row names, cell types from marker_mat as column names

### Examples

    pbmc_mm <- matrixize_markers(pbmc_markers)

    pbmc_avg <- average_clusters(
        pbmc_matrix_small,
        pbmc_meta,
        cluster_col = "classified"
    )

    pbmc_avgb <- binarize_expr(pbmc_avg)

    compare_lists(
        pbmc_avgb,
        pbmc_mm,
        metric = "spearman"
    )

[Package clustifyr version 1.6.0 Index]