Commit 9fb07cfe authored by Marco Chierici's avatar Marco Chierici
Browse files

Added README; modified makefile

parent 07a8a816
### INF pipeline
**Requirements**
Python3 with mlpy (!), numpy, scikit-learn
R >= 3.2.3 with cvTools, doParallel, TunePareto, igraph
To install R via Anaconda: [doc](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/)
To install the R dependencies, run the following command from the R prompt:
`install.packages(c("cvTools", "doParallel", "TunePareto", "igraph"))`
**Input files**
* omics layer 1 data: 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**)
* 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**
The original pipeline was reimplemented in a Makefile, with variables that can be set runtime.
An example is given in the `runner.sh` script:
```
make -f run_INF_RF-KBest.mk \
OUTBASE=${OUT} \
# layer1 dataset
DATA1=data/AG1-G_145_LIT_ALL_tr.txt \
# layer2 dataset
DATA2=data/CNV-G_145_LIT_ALL_tr.txt \
# layer1 + layer2 juxtaposed dataset
FILE=data/AG1-G_CNV-G_145_LIT_ALL_tr.txt \
# sample labels
LABEL=data/label_145_ALL-EFS_tr.lab
```
......@@ -15,9 +15,9 @@ DATA2 ?= data/MAV-G_498_LIT_ALL_tr.txt
ENDPOINT ?= ALL-EFS
# added MF 20170710
THREADS ?= 4
OUTBASE ?= /path/to/out_tmp
BINDIR := /Users/chierici/Documents/work/inf_test
OUTBASE := /Users/chierici/Documents/work/inf_test/out_tmp
BINDIR := /path/to/repo
OUTDIR := $(OUTBASE)/$(ENDPOINT)
# derived variables
......
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