Commit 1f782e1f authored by Alessia Marcolini's avatar Alessia Marcolini
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Improve Input Files section, minor fixes

parent b19b3360
# Integrative Network Fusion (INF) # Integrative Network Fusion (INF)
![INF pipeline ](figs/INF_pipeline.jpeg) ![INF pipeline ](figs/INF_pipeline.jpeg)
Repository attached to the article "Integrative Network Fusion: a multi-omicsapproach in molecular profiling". Repository attached to the article "Integrative Network Fusion: a multi-omics approach in molecular profiling".
**Authors**: Marco Cherici*, Nicole Bussola*, Alessia Marcolini*, Margherita Francescatto, Alessandro Zandonà, Lucia Trastulla, Claudio Agostinelli, Giuseppe Jurman, Cesare Furlanello. **Authors**: Marco Cherici*, Nicole Bussola*, Alessia Marcolini*, Margherita Francescatto, Alessandro Zandonà, Lucia Trastulla, Claudio Agostinelli, Giuseppe Jurman, Cesare Furlanello.
...@@ -49,14 +49,12 @@ All the data used to perform the experiments has been published on [Figshare](dx ...@@ -49,14 +49,12 @@ All the data used to perform the experiments has been published on [Figshare](dx
## Usage ## Usage
**Input files** #### Input files
* omics layer 1 data: samples x features, tab-separated, with row & column names * Omics layer files: samples x features, tab-separated, with row & column names
* omics layer 2 data: same as above (**samples must be in the same order as the first file**) * Labels file: one column, just the labels, no header (**same order as the data files**)
* omics layers 1+2 data: the juxtaposition of the above two files
* labels file: one column, just the labels, no header (**same order as the data files**)
**Example run** #### Example run
The INF pipeline is implemented with a [Snakefile](https://snakemake.readthedocs.io/en/stable/index.html). The INF pipeline is implemented with a [Snakefile](https://snakemake.readthedocs.io/en/stable/index.html).
...@@ -71,7 +69,8 @@ All the {variables} can be specified either in a config.yaml file or on the comm ...@@ -71,7 +69,8 @@ All the {variables} can be specified either in a config.yaml file or on the comm
Example: Example:
```bash ```bash
snakemake --config datafolder=data outfolder=results dataset=tcga_brca target=ER layer1=gene layer2=cnv layer3=prot model=randomForest random=false split_id=0 -p snakemake --config datafolder=data outfolder=results dataset=tcga_brca target=ER \
layer1=gene layer2=cnv layer3=prot model=randomForest random=false split_id=0 -p
``` ```
This example showed an example pipeline using three omics layers from BRCA-ER dataset. You can use an arbitrary number of omics layers by adding or removing `layer` arguments accordingly. This example showed an example pipeline using three omics layers from BRCA-ER dataset. You can use an arbitrary number of omics layers by adding or removing `layer` arguments accordingly.
...@@ -88,4 +87,4 @@ The pipeline can be "dry-run" using the `-n` flag: ...@@ -88,4 +87,4 @@ The pipeline can be "dry-run" using the `-n` flag:
snakemake --cores 12 -n snakemake --cores 12 -n
``` ```
A bash script (`runner.sh`) is provided for convenience, in order to run the pipeline for each split, to compute Borda of Bordas and to average metrics for all the splits. *A bash script (`runner.sh`) is provided for convenience, in order to run the pipeline for each split, to compute Borda of Bordas and to average metrics for all the splits.*
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