get_bulk function

Produce combined bulk expression and allele profile

get_bulk(
  count_mat,
  lambdas_ref,
  df_allele,
  gtf,
  genetic_map = NULL,
  min_depth = 0,
  nu = 1,
  verbose = TRUE
)

Arguments

• count_mat: matrix Gene expression counts
• lambdas_ref: matrix Reference expression profiles
• df_allele: dataframe Allele counts
• gtf: dataframe Transcript gtf
• genetic_map: dataframe Genetic map
• min_depth: integer Minimum coverage to filter SNPs
• nu: numeric Phase switch rate
• verbose: logical Whether to print progress

Returns

dataframe Pseudobulk gene expression and allele profile

Examples

bulk_example = get_bulk(
    count_mat = gene_counts_example,
    lambdas_ref = ref_hca,
    df_allele = df_allele_example,
    gtf = gtf_hg38)