# RFLOMICS input format

RFLOMICS can handle three types of omics (transcriptomics (RNAseq), proteomics and metabolomics) and several datasets per omics generated from similar experimental design. Each dataset must have a complete design.

Below each input file is detailed.

## Experimental design file

This file provides the experimental design table. The first column indicates the sample names. Next columns indicate experimental conditions (called biological factors or technical/batch factors) and metadata (optional). Each row describes a sample by specifying the level for each experimental condition. This file is edited by the user and must contain a header with column names corresponding respectively to the factor names and metadata names.

It is advised that each factor’s level starts with a letter (for example, for a factor called Month, it is better to write M1 rather than 1).

## Omics data file

For each omics: The matrix-like file with abundance of omics data is needed. The first column indicates feature names (genes, proteins, or metabolites), column headers indicate the sample names.

### Transcriptomics (RNAseq counts data)

For RNAseq data the values correspond to raw read counts per genes or transcripts.

### Proteomics data

For proteomics data the values correspond to intensity of proteins.

### Metabolomics data

For metabolomics data the values correspond to intensity of metabolites.

## Annotation of features (optional)

This file contains annotation about biological functions of genes/proteins/metabolites, or their implication in biological pathways. This annotation is needed to compute Over Representation Analysis (ORA). This file must contain at least 2 columns, names of features (identical to the ones used in the abundance matrix) and term identifiers (ex. GO term accession : GO:0034599). It is possible to add 2 more columns: names of terms (ex. cellular response to oxidative stress) and the domain of annotation (ex. biological_process).

Gene ID | GO term accession | GO term name | GO domain
--- | --- | --- | ---
AT4G36648 | GO:0006412 | translation | biological_process
AT4G36648 | GO:0030533 | triplet codon-amino acid adaptor activity | molecular_function
AT1G18745 | GO:0006396 | RNA processing | biological_process
AT1G18745 | GO:0005730 | nucleolus | cellular_component
AT3G00980 | GO:0006396 | RNA processing | biological_process
AT3G00980 | GO:0005730 | nucleolus | cellular_component