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Importing PBAT Family-Based Data

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3.12 Importing PBAT Family-Based Data

Preparing Family Data

SVS supports the import of family-based data in FBAT/PBAT Pedigree format, FBAT/PBAT Phenotype format, text pedigree format, and family-based text phenotype format.

NOTE:

  • SVS also supports joining family-based spreadsheets with other spreadsheets. This may be useful if the genetic data for your family-based study comes from sources such as the Affymetrix GeneChip™.

The format of a text pedigree should be as follows:

  • The optional label column, whose position in the file you may specify in the import dialog, is mainly useful for indexing into other genetic data. This data could be, for instance, Affymetrix GeneChip™ data.
  • The first column after the row labels should be the family number or family ID.
  • The second column after the row labels should be the patient number or individual ID.
  • The third column after the row labels should be the father number or father ID.
  • The fourth column after the row labels should be the mother number or mother ID.
  • The fifth column after the row labels should be the gender. Gender should be encoded as 0 = missing, 1 = male, 2 = female. If the encoding 0 = male, 1 = female is used, set ? or the appropriate character as the missing value encoding on the Advanced Options tab.
  • The sixth column after the row labels should be the affection status. Affection should be encoded as 0 = unknown, 1 = unaffected, 2 = affected. If the encoding 0 = unaffected, 1 = affected is used, set ? or the appropriate character as the missing value encoding on the Advanced Options tab.
  • The remaining columns should be genetic markers or any other phenotypic data.

The format of a text phenotype should be as follows:

  • The first column after the row labels should be the family number or family ID.
  • The second column after the row labels should be the patient number or individual ID.
  • The remaining columns should be phenotypic data or genetic markers.
Import FBAT Pedigree

[Picture]

Figure 18: FBAT Pedigree Import Window

In the Import FBAT Pedigree File dialog (see Figure 18), select the pedigree file (file with the .ped extension) by clicking on Browse and navigating through the file manager to the desired file. You may edit the dataset name at this time. You may also change the default missing encoding options by clicking on the Advanced Options tab and indicating the value that your file uses for missing phenotype and or missing genotype.

Import FBAT Phenotype

[Picture]

Figure 19: FBAT Phenotype Import Window

In the Import FBAT Phenotype File dialog (see Figure 19), select the phenotype file (file with the .phe extension) by clicking on Browse and navigating through the file manager to the desired file. You may edit the dataset name at this time. You may also indicate a custom encoding for missing data by clicking on the Advanced Options tab and indicating the character that your phenotype file uses for missing data.

Import Text Pedigree

[Picture]

Figure 20: Text Pedigree Import Window

In the Import Text Pedigree dialog (see Figure 20), select the text pedigree file by clicking on Browse and navigating through the file manager to the desired text file. You will need to indicate how the text file is delimited in the drop down menu. Possible options are comma, white-space, tab delimited or “Other ->”. If your text file uses a different delimiter than comma, space or tab, select other and indicated the character used in the text box to the right of the menu. You have the option of generating row labels from the Patient ID and Family ID columns or by using the first column in the text file. On the Advanced Options tab you can indicate a custom encoding for missing data by entering in the string used for missing values in the text box. You can also change the allele delimiter if your text file uses a character different from the default underscore (_). There are several possible options and also an “Other ->” category where you can specify the character used to the right of the menu. If there are header lines in your text file you can skip them by checking in the appropriate box and indicating the number of rows in the header of the file.

Import Text Phenotype

[Picture]

Figure 21: Text Phenotype Import Window

In the Import Text Phenotype dialog (see Figure 21), select the text phenotype file by clicking on Browse and navigating through the file manager to the desired text file. You will need to indicate how the text file is delimited in the drop down menu. Possible options are comma, white-space, tab delimited or “Other ->”. If your text file uses a different delimiter than comma, space or tab, select other and indicated the character used in the text box to the right of the menu. You have the option of generating row labels from the Patient ID and Family ID columns or by using the first column in the text file. On the Advanced Options tab you can indicate a custom encoding for missing data by entering in the string used for missing values in the text box. You can also change the allele delimiter if your text file uses a character different from the default underscore (_). There are several possible options and also a “Other ->” category where you can specify the character used to the right of the menu. If there are header lines in your text file you can skip them by checking in the appropriate box and indicating the number of rows in the header of the file.

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