make_group_bulks: Make a group of pseudobulks

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

Make a group of pseudobulks

Description

Make a group of pseudobulks

Usage

make_group_bulks(
  groups,
  count_mat,
  df_allele,
  lambdas_ref,
  gtf,
  min_depth = 0,
  nu = 1,
  segs_loh = NULL,
  ncores = NULL
)

Arguments

groups	list Contains fields named "sample", "cells", "size", "members"
count_mat	dgCMatrix Gene counts
df_allele	dataframe Alelle counts
lambdas_ref	matrix Reference expression profiles
gtf	dataframe Transcript GTF
min_depth	integer Minimum allele depth to include
segs_loh	dataframe Segments with clonal LOH to be excluded
ncores	integer Number of cores

Value

dataframe Pseudobulk profiles

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