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

In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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
)

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)

numbat documentation built on May 29, 2024, 1:29 a.m.