imputation: Metabolomic Dataset Imputation

In AurelieGuilbault/VIQCing: Data Processing For Metabolomic Data

Description

Impute the given dataset with different method options. Produces <filename>_imputed.txt, containing the imputed dataset; See Details for available Imputation Methods

Usage

imputation(file, k = 2, method = "knn", npcs = 3, sigma = 0.1,
  nTree = 30, na.string = "NA", transformation = "None",
  compound = NULL, metabolite = NULL, sampleStart = 3)

Arguments

file	file containing the dataset to impute; a column "Compound"; a column "Metabolite"; and all the columns sample from <sampleStart> to the end of the file; the rest doesn't matter and the names are optional, as long as the column position is entered.
k	default 2, the k used for the knn imputation;
method	default "knn", the chosen method for replacing the missing values. Can be "knn", "RF", "QRILC", "SVD", "mean", "median", "HM" or "0". See Details.
npcs	default 3, npcs for SVD method;
sigma	default 0.1, tune sigma parameter for QRILC method;
nTree	default 30, number of tree for the RF method;
na.string	default "NA", string to consider as NA in the dataset;
transformation	default "None", can be "scale" or "log";
compound	default NULL, position of the compound column if named otherwise;
metabolite	default NULL, position of the metabolite column if named otherwise;
sampleStart	default 3, 1st column of the actual data;

Details

Available imputation methods:

• "knn": From the impute package, use the k nearest neighboors to impute the values;

• "RF": From the missForest package, use RandomForest algorithm to impute the values;

• "QRILC": From the imputeLCMD package, use Quantile regression to impute the values;

• "SVD": From the pcaMethods package, use SVDimpute algorithm as proposed by Troyanskaya et al, 2001. to impute the values;

• "mean","median", ""median", "0", "HM": simple value replacement, either by the mean, median, 0 of Half minimum of the row;

Value

df, the imputed dataset as a dataframe.

See Also

• impute packagehttps://www.rdocumentation.org/packages/impute

• missForest package https://www.rdocumentation.org/packages/missForest

• imputeLCMD package https://www.rdocumentation.org/packages/imputeLCMD

• pcaMethods package https://www.rdocumentation.org/packages/pcaMethods

Examples

for a dataset with the following header ; Compound, m/z, Metabolite, RT, Sample #1, ...
imputation("dummySet.tsv", method="knn", transformation="log", sampleStart=5)

for a dataset with the following header ; compound, m/z, metabolite, RT, Sample #1, ...
imputation("dummySet.tsv", method="knn", transformation="log", metabolite = 3, compound = 1, sampleStart=5)

AurelieGuilbault/VIQCing documentation built on Oct. 30, 2019, 5:02 a.m.