Data retrieval: Formats - Linkage

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This section generates a properly formatted Linkage file:

What you need to do is as follows:

1. Enter a Description to identify the process.

2. Select which of the SNPs in your Study are going to be used. You can do it in several ways:

- By position: You can specify a chromosome and a start and end positions which delimit a region you are interested in.

- By Region: Depending on the content of the field "Region" in your SNPs Table.

- By Gene: Depending on the content of the field "Gene" in your SNPs Table.

- All: All SNPs in your Study will be selected.

3. Enter information about sex and affection of samples  in order to create a linkage format file.

In the sex definition boxes, just introduce values defining sex as they are in the "sex" field of the Samples Table.

In the Case/Control boxes,

- Select the field of the Samples Table that defines cases and controls:

- Then you need to select the proper values for cases and controls:

Samples with values other than the ones declared here will be discarded and not used in the process.

When more than two possible values exist in a field. You may want to enter only one of those values in either the "Case" or the "Control" boxes, leaving the other box untouched (that is, leaving the "[Select Item]" option there). By doing so, those samples that match your explicit selection are being defined as, say, Cases (or Controls, if you selected so). All the remaining samples having other values will be used as Controls.

If a blank is selected " ", that means that there are Samples with no value in the field and that those are being selected as a case or control.

4. You can select Batch mode.

This is a fundamental time-saving feature. Selecting one of the fields in the Samples or SNP table, SNPator will run this process as many times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you have defined your samples in the "sex" field as "M" or "W", selecting "sex" as the attribute of the Sample batch mode will result in having two runs of the Linkage format retrieval, taking separately men and women.

If you select at the same time sample and SNP batch fields, you are going to obtain as many runs of the process as all possible combinations of the values of samples and SNPs in the fields you selected.

5. After this, the "Retrieve Data" button has to be pressed and the resulting file will appear in the User results section. There should be a *.zip file containing:

- snps.txt

List of SNPs with their positions in the format required by Haploview

- linkageFormatReport.txt

The file with Linkage format.

- information.txt

SNPator information to identify the job: date, time, user, study and filter.

- Haploid data treatment.

Currently, only diploid genotypes are being supported.