LoadingVCF_typewise — LoadingVCF

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.

samples_path
patient
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,
  cells_include = NULL,
  cells_exclude = NULL,
  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.
cells_include: A vector of cell barcodes. Only these cells will be retained.
cells_exclude: A vector of cell barcodes. These cells will be removed from the output.
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