numbat (version 1.4.2)

get_bulk: Aggregate single-cell data into combined bulk expression and allele profile

Description

Aggregate single-cell data into combined bulk expression and allele profile

Usage

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

Value

dataframe Pseudobulk gene expression and allele profile

Arguments

count_mat

dgCMatrix Gene expression counts

lambdas_ref

matrix Reference expression profiles

df_allele

dataframe Single-cell allele counts

gtf

dataframe Transcript gtf

subset

vector Subset of cells to aggregate

min_depth

integer Minimum coverage to filter SNPs

nu

numeric Phase switch rate

segs_loh

dataframe Segments with clonal LOH to be excluded

verbose

logical Verbosity

Examples

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