Createobj: Generate Alleloscope object for analysis

Description Usage Arguments Value

View source: R/Createobj.R

Description

Generate Alleloscope object for analysis

Usage

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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 Feb. 21, 2022, 9:57 a.m.