read.strtc1.bams: Read in cell-specific bam files for STRT/C1

In sqjin/nlvelo: RNA velocity estimation using nonlinear models

Description

Read in cell-specific bam files for STRT/C1

Usage

read.strtc1.bams(
  bam.files,
  annotation.file,
  min.exon.count = 100,
  n.cores = defaultNCores(),
  min.umi.reads = 1
)

Arguments

bam.files	list of bam files (one per cell)
annotation.file	gene annotation refFlat file
min.exon.count	minimum number of molecules (across all cells) for the exon to be considered expressed
n.cores	number of cores to use
min.umi.reads	minimum number of read required per UMI/gene combination to be counted (defaults to 1)

Value

a list structure analogous to the return of read.smartseq2.bams(), counting molecules instead of reads.

sqjin/nlvelo documentation built on Feb. 11, 2021, 8:09 a.m.