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Get list of analyses classified as technical outliers

Source: R/data-outlier.R
detect_outlier.Rd

Retrieves analysis IDs of data outliers based the principal components PCA with SD or MAD fences

Usage

detect_outlier(
  data = NULL,
  variable,
  filter_data,
  qc_types = c("BQC", "TQC", "SPL"),
  pca_component,
  fence_multiplicator,
  summarize_fun = c("pca", "rma"),
  outlier_detection = c("sd", "mad"),
  log_transform = TRUE
)

Arguments

data

MidarExperiment object

variable

Feature variable used for outlier detection

filter_data

Use all (default) or qc-filtered data

qc_types

QC types included in the outlier detection

pca_component

PCA component to be used

fence_multiplicator

Multiplicator for SD or MAD, respectively.

summarize_fun

Function used to summarize the features, either "pca" based on PCA, or "rma" based on mean relative abundance (RMA) of all features

outlier_detection

Outlier detection method, either based on "sd" or "mad"

log_transform

Log-transform data for outlier detection

Value

MidarExperiment object