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NormalizeMets (version 0.25)

Analysis of Metabolomics Data

Description

Metabolomics data are inevitably subject to a component of unwanted variation, due to factors such as batch effects, matrix effects, and confounding biological variation. This package is a collection of functions designed to implement, assess, and choose a suitable normalization method for a given metabolomics study (De Livera et al (2015) ).

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Version

Install

install.packages('NormalizeMets')

Monthly Downloads

36

Version

0.25

License

GPL (>= 2)

Last Published

March 23rd, 2018

Functions in NormalizeMets (0.25)

Didata

Direct infusion mass spectrometry metabolomics dataset
CompareRlaPlots

CompareRlaPlots
ComparePcaPlots

Compare PCA Plots
Dendrogram

Dendrogram
ComparePvalHist

p-value Histogram
CompareVolcanoPlots

Compare Volcano plots
GenerateReport

Generate Report
NormScaling

Normalisation methods based on scaling
LinearModelFit

Linear models
PcaPlots

PCA plots
HeatMap

Heat map
NormalizeMets-package

NormalizeMets package
LogTransform

Log transformation
RlaPlots

RLA plots
NormQcmets

Normalisation methods based on quality control metabolites
UVdata

A designed metabolomics dataset
alldatacheck

Check all data
VolcanoPlot

Volcano plot
NormQcsamples

Normalisation methods based on quality control samples
dataview

Data Viewing
VennPlot

Venn Diagram
alldata-class

Metabolomic alldata- class
ContrastMatrix

Contrast matrix
multiplot

Multiple plot function ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
Corr

Computes correlation matrix for a metabolomics dataset or compares the correlation between two metabolomics datasets
editcolnames

Edit column names of a metabolomic data matrix
alldataC

A designed metabolomics dataset
uv_ruvrandclust

The UVdata normalized by the RUV random for clustering method
alldata_eg

LC-MS metabolomics dataset
MissingValues

Missing value replacement
featuredata_roots

A metabolomics dataset analyzed by GC-TOF/MS.
NormCombined

Normalisation methods based on a combination of methods
SvmFit

support vector machine
ToInputdata

Convert to Inputdata
metgroupCheck

Check data compatibility
mixdata

A designed metabolomics dataset