Createobj: Generate Alleloscope object for analysis

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

Generate Alleloscope object for analysis

Description

Generate Alleloscope object for analysis

Usage

Createobj(
  alt_all = NULL,
  ref_all = NULL,
  var_all = NULL,
  samplename = "sample",
  genome_assembly = "GRCh38",
  dir_path = "./",
  barcodes = NULL,
  size = NULL,
  assay = "scDNAseq",
  cov = FALSE
)

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 matrix with two columns: col1: different chromosome; col2: for the size (bp) of different chromosomes.
assay	A character indicating the type of sequencing data. (ex: "scDNAseq" or "scATACseq")
cov	Logical (TRUE/FALSE). Whether or not to use only coverage. If "cov" is TRUE, alt_all, ref_all, andvcf_all are not required.
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.