preprocess: Preprocess metabolomics data

In chechir/phantomR: Provide functions for visualisation and notmalisation of Metabolomics data

Description

Preprocess: perform sparsity removal or features under the threshold and impute according to a given function

Usage

preprocess(
  df,
  mf_ids,
  sparsity_threshold = 0.2,
  imputation_func = min,
  imputation_ratio = 0.5
)

Arguments

df	Input data frame
imputation_func	function to impute values. e.g. median, min, etc
imputation_ratio	ratio to apply to values returned by the imputation function.
mf_cols	Input name of molecular features columns
sparsity_thershold	Only keep MFs where the sparsity is higher that the given threshold

Author(s)

BDA Team matias.thayer@owlstone..co.uk BDA Team License: GNU GPL (>= 2)

chechir/phantomR documentation built on June 17, 2020, 3:40 p.m.