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Martina Marba, 05/30/2010 10:55 am


Association Analysis input form

Online examples

Here you can load small datasets from our server. You can use them to run examples and see how the tool works. Click on the links to load the data.

  • Example1: Association analysis: chi-square test The zip file contains the ped and map files. With this analysis we can study whether there is association between SNPs and case/control samples using the chi-squared test.
  • Example2: Association analysis: fisher test The zip file contains the ped and map files. With this analysis we can study whether there is association between SNPs and case/control samples using the fisher test.

Data

The data we need to work out with should be in a compressed archive containing two (a ped and a map) files. PED and MAP files are plain text files; PED files contain genotype information (one person per row) and MAP files contain information on the name and position of the markers in the PED file.
Babelomics can read .zip, .gz and .tar.gz files but needs to be able to uncompressed data without finding any folder structure.

There are two ways to choose data, one selecting from the browse server where one should have previously uploaded data, or secondly, directly uploading data clicking on the Upload [genotype] label and then selecting the data from its computer.

Association test

We need to select one of the following tests:
  • Chi-square case/control: to test whether there is association between the two classification variables (phenotype and genotype). (To know whether to reject the null hypothesis that there is no association between variables).
  • Fisher's exact: this test is similar than the Chi-square test but in the case of to have a small sample size, it is better to use Fisher's exact test than Chi-squared.
  • Linear: this test allows for multiple covariates when testing for quantitative trait SNP association, and for interactions with those covariates.
  • Logistic: the logistic regression test is similar than the linear but instead of testing for quantitative trait it is for disease trait SNP association.
  • TDT: we will use this test only for family-based association (eg. trios) testing for disease traits.

Minor allele frequency

The minor allele frequency (MAF value) is used to filter SNPs on the basis of MAF value, it means only include SNPs with MAF >= "MAF value". The default value is 0.02.

This quantity is based only on founders (i.e. individuals for whom the paternal and maternal individual codes are both 0).

Job

  • Job name. Give a short name to your analysis job
  • Job description. You can use this section to document further the characteristics of this analysis

Its aim is to help you identifying the analysis you are running and distinguishing between several analysis.
To set the name is mandatory but you can leave the description empty if you do not want to use it.

Run

Once all options are set you can run the job. You may get some error message if some parameters are not properly set. If you do, just check the options you have chosen.

See Output form section for details on the result data format and plots.