assess_rank_bias: Find rank bias

Description Usage Arguments Value Examples

View source: R/utils.R

Description

Find rank bias

Usage

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assess_rank_bias(
  avg_mat,
  ref_mat,
  query_genes = NULL,
  res,
  organism,
  plot_name = NULL
)

Arguments

avg_mat

average expression matrix

ref_mat

reference expression matrix

query_genes

original vector of genes used to clustify

res

dataframe of idents, such as output of cor_to_call

organism

for GO term analysis, organism name: human - 'hsapiens', mouse - 'mmusculus'

plot_name

name for saved pdf, if NULL then no file is written (default)

Value

pdf of ggplot object

Examples

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## Not run: 
avg2 <- average_clusters(
    pbmc_matrix_small, 
    pbmc_meta$seurat_clusters
)
res <- clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    ref_mat = cbmc_ref,
    query_genes = pbmc_vargenes,
    cluster_col = "seurat_clusters"
)
call1 <- cor_to_call(
    res,
    metadata = pbmc_meta,
    cluster_col = "seurat_clusters",
    collapse_to_cluster = FALSE,
    threshold = 0.8
)
res_rank <- assess_rank_bias(
    avg2, 
    cbmc_ref, 
    res = call1
)

## End(Not run)

NCBI-Hackathons/RClusterCT documentation built on July 20, 2021, 3:15 p.m.