LoadingMAEGATK_typewise: LoadingMAEGATK_typewise

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

LoadingMAEGATK_typewise

Description

We load the MAEGATK output and transform it to be compatible with the VarTrix output. The input file is a specifically formated csv file with all the necessary information to run the analysis. Note that the source column in the input file needs to be mgaetk or mgatk for this function. This is case insensitive. 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. barcodes_path

3. patient

4. samples_file = NULL

Usage

LoadingMAEGATK_typewise(
  samples_file,
  patient,
  samples_path = NULL,
  patient_column = "patient",
  type_use = "scRNAseq_MT",
  chromosome_prefix = "chrM",
  min_cells = 2,
  cells_include = NULL,
  cells_exclude = NULL,
  barcodes_path = NULL,
  cellbarcode_length = 18,
  verbose = TRUE
)

Arguments

samples_file	Path to the csv file with the samples to be loaded.
patient	The patient you want to load.
samples_path	Path to the input folder.
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.
chromosome_prefix	The prefix you want use. Default: "chrM"
min_cells	The minimum number of cells with coverage for a variant. Variants with coverage in less than this amount of cells are removed. 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.
barcodes_path	Path to the barcodes file tsv. Default = NULL
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

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.