get_bulk {hahmmr}

Produce combined bulk expression and allele profile

Description

Produce combined bulk expression and allele profile

Usage

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

Value

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)