QC_pipeline_df: quality control pipeline for a simplified data.frame.

In XikunHan/metabolomicsR: Tools for Metabolomics Data

quality control pipeline for a simplified data.frame.

Description

This function will run QC steps on a simplified data.frame.

Usage

QC_pipeline_df(
  object,
  filter_column_constant = TRUE,
  filter_column_missing_rate_threshold = 0.5,
  filter_row_missing_rate_threshold = NULL,
  replace_outlier_method = "winsorize",
  nSD = 5,
  impute_method = "half-min",
  run_batch_norm = FALSE,
  run_transform = "scale",
  verbose = TRUE
)

Arguments

object	A data.frame object, first two columnns are ID and Batch.
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".
run_batch_norm	Whether run run_batch_norm ('batch_norm_df')
run_transform	Specify the transform method ('transformation'), eg. "log", "pareto_scale", "scale", "inverse_rank_transform". A User defined method is also supported.
verbose	print log information.

Value

A Metabolite object after QC.

XikunHan/metabolomicsR documentation built on Feb. 7, 2024, 1:17 p.m.