remove_samples: Remove samples based on different criteria

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Remove samples based on different criteria

Description

Remove samples with large frequency of missing values (method = "missing") or low expression (method = "detection.pvalue" or method = "zero").

Usage

remove_samples(se, assay = 1, method, freq = 0.5, verbose = FALSE)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay to be used for filtering.
method	Method to determine samples to be removed: "missing", "detection.pvalue", "zero".
freq	Numeric. If more than freq*100 % of the genes fulfill criterion, the sample is removed.
verbose	Logical. Should number of removed samples be reported?

Value

RangedSummarizedExperiment-class object with samples removed

Examples

library(recount)
data("rse_gene_SRP009615")

rse_gene_SRP009615 = remove_samples(se = rse_gene_SRP009615,
                                    method = "zero",
                                    freq = 0.4)

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.