qc_and_filter: QC_and_Filter

In EDePasquale/Ericas_Functions: A Package of Erica's Most Used Functions for Processing Data Plus Random Utilities

Description

This function allows you to provide a list of paths leading to the QC sample sheet (Erica's pipeline Step 4) to perform quality control and filtering.

Usage

qc_and_filter(
  directories,
  genome = "GRCh38",
  suffix = "default",
  min.umis = 500,
  min.genes = 250,
  max.mito = 0.3,
  sig = T,
  dense = F
)

Arguments

directories	List of directories containing CellRanger output for QC and filtering. Example single directory path is "/Volumes/broad_vangalenlab/depasquale/CellRanger/210628_GeneCounts"
genome	Desired genome: "GRCh38" and "GRCm38" are accepted, default is "GRCh38"
suffix	Suffix for directory where the output of this function will be stored and where the input sample sheet is located. Default is the "QC" suffix.
min.umis	QC filter for minimum number of Unique Molecular Identifiers (UMIs) detected per cell. Default is 500
min.genes	QC filter for minimum number of genes detected per cell. Default is 250
max.mito	QC filter to remove cells that exceed this fraction of mitochondrial alignments. Default is 0.3
sig	Boolean for whether or not to plot cell type signatures. Default is T
dense	Boolean for whether or not to save dense matrices alongside sparse matrices. Default is F

Examples

qc_and_filter()

EDePasquale/Ericas_Functions documentation built on Dec. 17, 2021, 5:38 p.m.