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PBAT Family-Based QC Statistics

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7.5 PBAT Family-Based QC Statistics

The quality control statistics for family-based studies are used to measure the genotyping error rate of each proband in a family individually. See [Fardo 2009].

[Picture]

Figure 37: PBAT Family-Based QC Window
Data Requirements

PBAT family-based QC statistics require a pedigree dataset containing genotypic data. First, import your data into a SVS project (See Importing Your Data Into A Project). The family-based statistics dialog can be accessed by selecting Quality Assurance > PBAT Family-Based QC from the spreadsheet menu.

Processing

Select computation parameter and output options and select the Run button to process. Descriptions of the computation parameters and output options are detailed below.

One spreadsheet of results will be created as a child of the current spreadsheet navigator window node. Information about the parameters used will be recorded in the node annotations log.

Computation Parameters

Algorithm

If the Use alternative rapid pedigree algorithm IS NOT selected then the standard PBAT algorithm for processing extended pedigrees is used and Mendelian errors will not be calculated.

If the Use alternative rapid pedigree algorithm IS selected (the default) then the alternative rapid pedigree algorithm for processing extended pedigrees will be used and Mendelian errors will be calculated. See Phenotype and Haplotype Parameters for more information.

Number of non-founders in one pedigree

Enter the maximum number of non-founders plus one that exist in one pedigree. “Non-founders” refers to subjects in the pedigree who have parents whose data is also in the pedigree. If a pedigree is found to have this number of non-founders or more, it will not be processed. For instance, if the user wants to restrict pedigrees to only have two siblings plus their parents, then enter 3 in this box.

NOTE:

  1. Under the alternative rapid pedigree algorithm, this parameter refers to the maximum of non-founders within the family clusters identified by this algorithm, rather than to the maximum number of non-founders within any original extended pedigree.
Output

Output by marker

The rows will correspond to markers and the columns in the output spreadsheet will be:

  • MAF: Minor Allele Frequency for the specified marker.
  • Mendelian errors: Number of Mendelian errors for the specified marker.
    • NOTE: This column will only display if the alternative rapid pedigree algorithm was selected.
  • HW: Hardy-Weinberg Equilibrium value for the specified marker.
  • FBATS: Sum of the transmission scores for the specified marker that would occur if a TDT test were to be done in which all probands were assumed to be “affected”, and the null hypothesis were “no linkage and no association”.
  • FBATV: Sum of terms of the variance matrix for the specified marker that would occur under the above-mentioned test.
  • FBATV2: Sum of squares of the transmission scores over the probands for the specified marker that would occur under the above-mentioned test.

Output by proband

This is the default output selection.

The rows will correspond to probands and the columns in the output spreadsheet will be:

  • # Markers: The number of markers used for the calculation
  • Mendelian errors: Number of Mendelian errors for the specified proband.
    • NOTE: This column will only display if the alternative rapid pedigree algorithm was selected.
  • Tgw p-value: P-value of the standardized genome-wide transmission statistic. This statistic follows an approximate χ2 distribution with one degree of freedom.
  • Tgw: Standardized genome-wide transmission statistic. A value of greater than 30 for this statistic may indicate substantial amounts of genotyping error in the data for this proband.
  • E(delta X): Expected Mendelian residual.
  • var(delta X): Variance of the Mendelian residual.

Output all details

The rows will correspond to markers and the columns in the output spreadsheet will be:

  • MAF: Minor Allele Frequency for the specified marker.
  • Mendelian errors: Number of Mendelian errors for the specified marker.
    • NOTE: This column will only display if the alternative rapid pedigree algorithm was selected.
  • HW: Hardy-Weinberg Equilibrium value for the specified marker.
  • FBATS: Sum of the transmission scores for the specified marker that would occur if a TDT test were to be done in which all probands were assumed to be “affected”, and the null hypothesis were “no linkage and no association”.
  • FBATV: Sum of terms of the variance matrix for the specified marker that would occur under the above-mentioned test.
  • FBATV2: Sum of squares of the transmission scores over the probands for the specified marker that would occur under the above-mentioned test.
  • Columns for probands: A column for every proband. Each value listed is the contribution to the FBATS statistic and to the Tgw statistic for the specified proband and specified marker.
    • NOTE: A missing value in any cell of this column indicates that there was a Mendelian error for this proband with this marker’s data.

Output -log 10 p-values

These values are only available for Output by proband and calculates the −log 10(Tgw p-value) for every proband.

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