# Postprocessing and univariate analysis of omics data

## Documentation for package ‘phenomis’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

phenomis-package | Postprocessing and univariate analysis of omics data
annotating | MS annotation
annotating-method | MS annotation
annotating_parameters | MS annotation
clustering | clustering
clustering-method | clustering
correcting | correcting
correcting-method | correcting
filtering | Filtering of the features (and/or samples) with a high proportion of NAs or a low variance
filtering-method | Filtering of the features (and/or samples) with a high proportion of NAs or a low variance
gg_barplot | Barplot with ggplot2
gg_boxplot | Boxplot with ggplot2
gg_pie | Pie with ggplot2
gg_volcanoplot | Volcano plot with ggplot2
hypotesting | Univariate hypothesis testing
hypotesting-method | Univariate hypothesis testing
inspecting | Inspecting
inspecting-method | Inspecting
normalizing | Normalization of the data matrix intensities
normalizing-method | Normalization of the data matrix intensities
phenomis | Postprocessing and univariate analysis of omics data
reading | reading
reducing | Grouping chemically redundant MS1 features
reducing-method | Grouping chemically redundant MS1 features
transforming | Transformation of the data matrix intensities
transforming-method | Transformation of the data matrix intensities
vennplot | Venn diagram with VennDiagram
writing | Exporting a SummarizedExperiment (or MultiAssayExperiment) instance into (subfolders with) the 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', 'variableMetadata.tsv'
writing-method | Exporting a SummarizedExperiment (or MultiAssayExperiment) instance into (subfolders with) the 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', 'variableMetadata.tsv'