Postprocessing and univariate analysis of omics data

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Documentation for package ‘phenomis’ version 1.15.6

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

phenomis-package	Postprocessing and univariate analysis of omics data
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_corplot	Regression plot 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
plot_hypotesting	Displays the volcano plot and the individual box plots (respectively, dot plots) after a two group statistical test (respectively, a correlation test) has been performed on a 'SummarizedExperiment' object.
plot_hypotesting-method	Displays the volcano plot and the individual box plots (respectively, dot plots) after a two group statistical test (respectively, a correlation test) has been performed on a 'SummarizedExperiment' object.
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'