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Tutorial OncodriveFM

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luzgaral edited this page Jan 31, 2015 · 6 revisions

General

Tutorial

Analysis tools

Worked examples

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INPUT


#### STEPS [1. Select your data](tutorial-oncodrivefm#select-your-data)
[2. Select priorizitation parameters](tutorial-oncodrivefm#select-priorizitation-parameters)
[3. Fill information job](tutorial-oncodrivefm#fill-information-job)
[4. Press *Launch job* button](tutorial-oncodrivefm#press-launch-job-button)

#### OUTPUT - [Input parameters](tutorial-oncodrivefm#input-parameters) - [Output files](tutorial-oncodrivefm#output-files)
#### CITE




INPUT

#####Input data

  • Input data should be a matrix upload as the data type VCF 4.0. See data types [here](Data Types).

#####Online example

  • Here you can load a small dataset from our server. You can use them to run this example and see how the tool works. Click on the links to load the data: BRCA cancer set from TCGA.

### STEPS #####Select your data First step is to select your data to analyze.

#####Select priorizitation parameters

  • Select Human Genome version: GRCh37 or GRCh38
  • Choose the global score estimator: median or mean.

#####Fill information job

  • Select the output folder
  • Choose a job name
  • Specify a description for the job if desired.

#####Press Launch job button Press launch button and wait until the results is finished. A normal job may last approximately few minutes but the time may vary depending on the size of data. See the state of your job by clicking the jobs button in the top right at the panel menu. A box will appear at the right of the web browser with all your jobs. When the analysis is finished, you will see the label "Ready". Then, click on it and you will be redirected to the results page.


### OUTPUT #### Input parameters In this section you will find a reminder of the parameters or settings you have used to run the analysis.

Output files

Significant results

Statistical information for significant genes: p-value and q-value.

## version=0.6.0
## date=2015-01-26 15:15:25
## slices=SIFT,PPH2,MA
## method=median-empirical
ID	PVALUE	QVALUE
ENSG00000125900,ENSG00000260861	0.999979770285	0.999979770285
ENSG00000101327	0.0142471618837	0.0376680894146
ENSG00000101307	0.0852333712501	0.113644495
ENSG00000196476	0.0188340447073	0.0376680894146

CITE

Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743 - Site - NAR - PubMed

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