metabolomicsR (version 1.0.0)

QC_pipeline: quality control pipeline

Description

This function will run QC steps on a Metabolite object

Usage

QC_pipeline(
  object,
  filter_column_constant = TRUE,
  filter_column_missing_rate_threshold = 0.5,
  filter_row_missing_rate_threshold = NULL,
  replace_outlier_method = NULL,
  nSD = 5,
  impute_method = "half-min",
  verbose = TRUE
)

Arguments

object

An object, data.frame, data.table or Metabolite.

filter_column_constant

A logical value, whether to filter columns (features) with a constant value.

filter_column_missing_rate_threshold

A numeric threshold to filter columns (features) below a missing rate, default: 0.5. Other values: 0.2, 0.8. If NULL, then skip this step.

filter_row_missing_rate_threshold

A numeric threshold to filter rows (samples) below a missing rate. Default: NULL, to skip this step. Other values: 0.5, 0.2, 0.8.

replace_outlier_method

Method to replace outlier value, see replace_outlier.

nSD

Define the N times of the SD as outliers.

impute_method

Imputation method, the default method is half the minimum value (`half-min`) of the metabolite. Currently support 'half-min', "median", "mean", "zero".

verbose

print log information.

Value

A Metabolite object after QC.