Tutorial

A tutorial for pediSNP users. Covers the analysis of Affymetrix, Illumina, HapMap, and custom format data

Each of the exported data types that pediSNP supports have slightly different formats. pediSNP has been designed to handle the differences in these formats, but the data must be exported in a way pediSNP can understand. Please select a tutorial to learn how to export data and run pediSNP.


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Affymetrix CNAT 4.0 Data Export

Illumina BeadStudio Data Export

HapMap Downloaded Data Export

Running pediSNP

Tips and Hints


Affymetrix CNAT 4.0 Data


Affymetrix data files are typically analyzed using the GeneChip Genotyping Analysis Software. This tutorial was written based on version 4.1.0.26, but should be applicable to older versions as well.

1. Open the Affymetrix GType software

2. In the data source panel choose "Analysis Results"
Affy Analysis Results

3. Double click on the appropriate "*.chp" files for the individuals you wish to analyze

4. Several columns are displayed for the data you have chosen. pediSNP will run faster if less extraneous data is displayed. Right click in the column headers for data other than Chromosome, Physical Position, the genotype calls and log2(ratio) (only needed if you answer Yes at Step 12) for the individuals of interest, and click the "Hide Column" option
Affy Hide Columns

5. Click the Export button from the toolbar

Affy Export Data

6. Choose an appropriate file name and save location. Be sure the "Export All" option is clicked and export the data

Affy Save File

7. Proceed with using the pediSNP tool as described below

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Illumina - BeadStudio


For SNPs genotyped using Illumina data the standard analysis software is BeadStudio. This portion of the tutorial will cover how to export data from BeadStudio for use with pediSNP.

1. Open your data file (typically *.bsc) with BeadStudio

2. Make sure you are in the Full Data Table

3. Using the Column Chooser be sure you have at least the following selected:

Illumina Column Chooser

From "Displayed Columns" show

  • Name
  • Chr
  • Position
  • The individuals of interest

From "Displayed Subcolumns" show

  • GType

4. Press the "Export Displayed Data to File" Button. Choose a save location and name. Export the data

Illumina Export Data

5. Sometimes the sample IDs are too long. To adjust the headers on a BeadStudio file open the exported file in a text editor. Change the genotype headers to whatever you wish to be displayed in the title of each individual's genotype plot and the overall title.

Note: Genotype columns of data exported from BeadStudio end in ".GType". This trailing ".GType" and "Log R Ratio" are automatically removed by pediSNP.

6. Proceed with using the pediSNP tool as described below

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HapMap - Downloaded Data



pediSNP can analyze data downloaded from the HapMap site. These data are very high density, and therefore have large files. The HapMap data should be run on a per chromosome basis. This portion of the tutorial will cover how to download HapMap data for use with pediSNP.

1. First go to the Downloads page at the International HapMap Project website


2. Click the "Genotypes" link from Bulk Data listing

HapMap Genotype Download

3. Pick the directory of the latest data for the build you wish to use

HapMap Build Selection

4. Pick the "non-redundant" folder of SNP data (you may or may not have to choose a strand first)


5. You should now see a list of files for each chromosome in each population. Select the chromosome and population you are interested in and click to download the file. The download will be a gzipped text file. On Linux and Mac systems the shell command "gunzip filename" should extract the text file from the archive. On Windows utility such as WinZip or WinRAR can extract the text file from the archive.

6. Proceed with using the pediSNP tool as described below

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Running pediSNP

The previous sections of this tutorial describe how to properly export data for use with pediSNP. This section will cover the use of the tool itself.

Input File


The first step in using pediSNP is to specify the file you want to analyze. By following the previous tutorials you should have a file exported in the proper format for your data type. Use the "Browse" button to locate this file. spache and tab are not allowed in the ID. R also requires variables to start with an alphabet. For IDs started with a numeric character, prefix them with an 'X' character in this pedigree table.

Pedigree Info


The second step is to provide the pedigree info of your data. The IDs in this step shall be the column headers in your input file, with the following suffix removed: '.loh_Call' for Affymetrix CNAT 4.0; '.GType' for Illumina; '_Call' in HapMap and all other cases.

Reversed Trios


The third step tell pediSNP where your would like to have the reverse-pedigree panels included in your output. If you choose No, the output will only include the normal (father + mother -> child) panels, one per child. In effect, you got the SNPtrio output. The panels from the reverse pedigree (child1 + child2 -> parent) can be groups in two ways: either paired panels of reversed father and reversed mother for each child, or, all reversed father panels followed by all reversed mother panels.



Data Source


Step four let you specify the source of your SNP text file. To reduce the file size, please select only the columns as indicated in Step 4.

Step five through Step fifteen are self explanatory.

Tips and Hints

If you need to manually edit any header information of large text files on a Windows PC, we suggest using a more advanced text/code editor than notepad, such as Crimson Editor or Notepad++. Mac and Linux text editors such as vi, emacs, and xemacs can usually open and manipulate large files with little problem.

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