dataFilter: Filter the dataset and remove genes and cells that could be...

In linquynus/RCAv2-beta: Reference Component Analysis

Description

Filter the dataset and remove genes and cells that could be of poor quality using user-defined thresholds

Usage

dataFilter(
  rca.obj,
  nGene.thresholds = c(100, NULL),
  nUMI.thresholds = c(1000, NULL),
  percent.mito.thresholds = c(0, 0.2),
  min.cell.exp = 10,
  plot = T,
  folderpath = ".",
  filename = "RCA_Filter.pdf"
)

Arguments

rca.obj	RCA object.
nGene.thresholds	numeric vector with lower and upper nGene thresholds
nUMI.thresholds	numeric vector with lower and upper nUMI thresholds
percent.mito.thresholds	numeric vector with lower and upper pMito thresholds
min.cell.exp	minimum number of cells a gene must be expressed in
plot	boolean - if True, plot data filter metrics
folderpath	path to save data filter metric plots to
filename	file name of saved plots

Value

RCA object.

linquynus/RCAv2-beta documentation built on Aug. 9, 2020, 12:34 a.m.