Rundf_dna: Run all steps for scDNA-seq data

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

Run all steps for scDNA-seq data

Description

Run all steps for scDNA-seq data

Usage

Rundf_dna(
  alt_all = NULL,
  ref_all = NULL,
  var_all = NULL,
  samplename = "sample",
  genome_assembly = "GRCh38",
  dir_path = "./",
  barcodes = NULL,
  size = NULL,
  assay = "scDNAseq",
  raw_counts = NULL,
  ref_counts = NULL,
  type = "tumor",
  cell_filter = 5,
  SNP_filter = 10,
  min_vaf = 0,
  max_vaf = 1
)

Arguments

alt_all	A SNP by cell read count matrix/ spare matrix for the alternative alleles.
ref_all	A SNP by cell read count matrix/ spare matrix for the reference alleles.
samplename	Sample name for the data.
genome_assembly	The genome assembly used for sequencing alignment. (ex: "GRCh38" or "GRCh37")
dir_path	Path of the output directory.
barcodes	A matrix/ data.frame with barcodes for each cell in the first column.
size	A numeric vector for the size (bp) of different chromosomes (with the names indicating which chromosome from 1 to 22)
assay	A character indicating the type of sequencing data. (ex: "scDNAseq" or "scATACseq")
raw_counts	A large binned coverage matrix (m1 bin by n1 cell) for all chromosomal regions of tumor sample.
ref_counts	A large binned coverage matrix (m2 bin by n2 cell) for all chromosomal regions of normal sample.
type	Specify whethere the sample is a "tumor" or "cellline". If "type" is a "cellline", param "ref_counts" needs to be specified for normal sample.
cell_filter	An integer of minimum cell number for SNP selection.
SNP_filter	An integer of minimum SNP number for cell selection.
min_vaf	A numerical value in the range (0,1) of minimum SNP variant allele frequency in the pseudo bulk for SNP selection.
max_vaf	A numerical value in the range (0,1) of mzsimum SNP variant allele frequency in the pseudo bulk for SNP selection.
vcf_all	A matrix/ data.frame of the vcf format for SNP information. (The length and order are the same as nrow(alt_all) and nrow(alt_all))

Value

A Alleloscope object including the necessary information.

seasoncloud/Alleloscope documentation built on March 17, 2023, 1:14 a.m.