| 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' |