get_bulk: Produce combined bulk expression and allele profile

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

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)

hahmmr documentation built on Oct. 26, 2023, 1:08 a.m.