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LoadingVCF_typewise

LoadingVCF_typewise.Rd

We load a cellwise pileup result from a VCF file. If you want to only load a single sample without the use of an input file, you have to set the following variables.

  1. samples_path

  2. patient

  3. samples_file = NULL

Note that the source column in the input file needs to be vcf for this function. This is case insensitive.

It has happened that reads with an N allele were aligned. This can cause problems since these variants are typically not in variants lists. We can remove all of these variants by setting remove_N_alternative to TRUE (the default). Set this option to FALSE, if you really want to retain these variants.

Usage

LoadingVCF_typewise(
  samples_file,
  samples_path = NULL,
  vcf_path,
  patient,
  patient_column = "patient",
  type_use = "scRNAseq_Somatic",
  min_reads = NULL,
  min_cells = 2,
  remove_N_alternative = TRUE,
  cellbarcode_length = 18,
  verbose = TRUE
)

Arguments

samples_file

Path to the csv file with the samples to be loaded.

samples_path

Path to the input folder.

vcf_path

Path to the VCF file with the variants.

patient

The patient you want to load.

patient_column

The column that contains the patient information. Use merge, if all samples should be merged.

type_use

The type of input. Only rows that have the specified type will be loaded.

min_reads

The minimum number of reads we want. Otherwise we treat this as a NoCall. Default = NULL.

min_cells

The minimum number of cells for a variant. Otherwise, we will remove a variant. Default = 2.

remove_N_alternative

Remove all variants that have N as an alternative, see Description. Default = TRUE

cellbarcode_length

The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18

verbose

Should the function be verbose? Default = TRUE