detect_duplicated_samples: Identification of duplicated samples

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

Identification of duplicated samples

Description

Detects duplicated samples with extremely high correlation of expression values using the function outlierFinder.

Usage

detect_duplicated_samples(
  se,
  assay = 1,
  title = NULL,
  use.fast = TRUE,
  remove.genes = TRUE,
  cor.method = "pearson",
  use = "everything",
  ...
)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay containing log transformed expression values.
title	Character. Title of the plot.
use.fast	Logical. Should fast implementation of covariance matrix estimation provided in the R package coop (default: TRUE).
remove.genes	Logical. Should genes with missing values be removed? (default: TRUE).
cor.method	Character. Correlation coefficient to be used ("pearson", "spearman" or "kendall"). Ignored if use.fast = TRUE.
use	Character. Method to deal with missing values as in cor and covar (default: "everything").
...	Additional arguments passed to the outlierFinder function.

Value

List with the following components:

• info: data.frame with identifiers of duplicated samples and their correlation or NULL

• plot: Histogram as returned by gghistogram

Examples

data("se.gene")

detect_duplicated_samples(se = se.gene)

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