find_rank_bias: Find rank bias

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

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
)

clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.