UMIQC: UMIQC

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

UMIQC

Description

We load the molecule_info.h5 file from CellRanger and plot the molecules by rank. A molecule is defined as a combination of UMI and CB. The molecules are ranked by their number of replicates.

Usage

UMIQC(
  central_input_file = NULL,
  molecule_info_path = NULL,
  subset_by_cbs = TRUE,
  cellbarcodes_path = NULL,
  umi_length = 12,
  min_reads = 100,
  sep = ",",
  samples_column = "sample",
  molecule_info_column = "molecule_info",
  cellbarcode_column = "cells",
  add_10x_suffix = "-1"
)

Arguments

central_input_file	Path to the csv file with the samples to be loaded.
molecule_info_path	Path to a single molecule_info file.
subset_by_cbs	Should the list of cell barcodes from the molecule_info.h5 file be subset to a list of approved cell barcodes? Default: TRUE
cellbarcodes_path	Path to a cell barcodes file. Not used if the central input file is used.
umi_length	The length of the UMI. Default = 12
min_reads	The minimum number of reads per molecule.
sep	The separator used in your samples_file. Default: ","
samples_column	The column for the samples in your samples_file. Default: "sample"
molecule_info_column	The column for the paths to the molecule_info files in your samples_file. Default: "molecule_info"
cellbarcode_column	The column for the paths to the cell barcodes files in your central input file. Default: "cells"
add_10x_suffix	Should a suffix be added to the cell barcodes? Default to the 10X standard: "-1"

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