get_bulk {numbat} | R Documentation |
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)
[Package numbat version 1.4.0 Index]