Aggregate single-cell data into combined bulk expression and allele profile — get_bulk • numbat

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
)

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

Value

dataframe Pseudobulk gene expression and allele profile

Examples

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