DATE OF BIRTH SORTING (DBSORT)

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1 DATE OF BIRTH SORTING (DBSORT) Release 3.1 December 1997

2 - ii - DBSORT

3 Table of Contents 1 Changes Since Last Release Purpose Limitations Command Line Parameters Input Parameter File (Logical Unit 1) Record 01: Title Record 02: Sorting Method Record 03: Records Per Individual Record 04: Family ID Record 05: Individual ID Record 06: Parent #1 ID Record 07: Parent #2 ID Record 08: Birth Order / Birth Year Record 09: Birth Month Record 10: Missing Value Codes Record 11: Month Convention Selection Record 12: User Specified Code for January Record 13: User Specified Code for February Record 14: User Specified Code for March Record 15: User Specified Code for April Record 16: User Specified Code for May Record 17: User Specified Code for June Record 18: User Specified Code for July Record 19: User Specified Code for August Record 20: User Specified Code for September Record 21: User Specified Code for October Record 22: User Specified Code for November Record 23: User Specified Code for December Family Data File (Logical Unit 11) Output Sorted Family Data File (Logical Unit 21) Information File (Logical Unit 22) Example Parameter File (Logical Unit 1) Family Data File (Logical Unit 11) Sorted Family Data File (Logical Unit 21) Information File (Logical Unit 22) iii -

4 - iv - DBSORT 7 Error Messages Information Messages Warning Messages Fatal Error Messages... 19

5 1 Changes Since Last Release Please see the Release Notes and Installation Guide for the most up to date information about program changes

6 - 2 - DBSORT

7 2 Purpose The purpose of DBSORT is to prepare data for input to FSP when the data will eventually be analyzed using the regressive class B and C models in the segregation analysis program REGC. DBSORT is designed to be a user-friendly program. It has two major tasks: 1. To sort the family data by either birth order or birth date, within the pedigree 2. To check for missing data. The first task of DBSORT is to sort the family data by either birth order or birth date within the pedigree. DBSORT does not change the format of data records. Each individual must have the following key information: 1. Family ID code 2. Individual ID code 3. Parent # 1 ID code 4. Parent # 2 ID code 5. Birth order or birth year 6. Birth month (optional) DBSORT puts individuals with missing birth information and unknown parents at the top of the sorted pedigree and puts those individuals with missing birth information and known parents at the bottom of the sorted pedigree. The second task of DBSORT is to identify: 1. Individuals with missing birth order or birth date but who have parents. 2. Individuals with missing birth order or birth date who are missing one parent. 3. Individuals with missing birth order or birth date who are missing both parents. 4. Individuals with missing birth order or birth date who have a sib or sibs. Individuals of types 1 to 3 above are identified to apprise the user of the location of missing data but action need not be taken to obtain birth order or birth data information. However, individuals of type 4 can cause errors in the results of segregation analysis using class B or C regression models because they will be treated as the youngest children in the sibship when this may not in fact be the case. Every effort should be made to obtain birth order or birth date information for these people. DBSORT should be rerun after these corrections are made and before running FSP

8 - 4 - DBSORT

9 3 Limitations 3.1 Command Line Parameters The current program contains a number of modifiable parameters whose dimensions can be increased to handle larger data sets. The parameters and their default maximum values are as follows: Description Parameter Default Value Number of individuals per family MAXIND 300 Number of records per individual MAXRPI 6 There are also the following constraints: 1) The minimum number of individuals per family is 2. 2) The maximum record length is ) The maximum field length of all key information is 8. Note: There is no limitation on the maximum number of families in the data set. The key information, described in the last section, can be located on any record of an individual and anywhere in a record. Please see the Release Notes and Installation Guide for details on how to adjust these parameters for your system

10 - 6 - DBSORT

11 4 Input The following set of records is used to determine the type of sample and analysis to be performed. 1. Parameter File - used to configure the program execution through parameter records. 2. Family Data File - the raw data file containing the Study ID, Family ID, Individual ID, Parents IDs, Sex and individual data. As the program uses the FORTRAN formatting rules, all integer-valued parameters must be right-justified in their fields on the input records, with no decimal point. All real-valued parameters should have a decimal point. The decimal point may be anywhere within the field and will override the given format. Variables read in A format may contain any valid alphanumeric characters. Any numeric fields left blank will be read as zeroes. 4.1 Parameter File (Logical Unit 1) There are 23 parameter records read in by DBSORT from logical unit 1. Records 1 to 11 are mandatory and records 12 to 23 are optional Record 01: Title A80 Blank Title of this run Record 02: Sorting Method A2 Method to be used in sorting the data file BO = sort according to birth order BY = sort according to birth year BD = sort according to birth month and year Record 03: Records Per Individual I1 Number of records per individual (Maximum = 6.) Record 04: Family ID I1 Record where the Family ID is located I5 Beginning column number of Family ID I5 Ending column number of Family ID Record 05: Individual ID I1 Record where the Individual ID is located I5 Beginning column number of Individual ID I5 Ending column number of Individual ID - 7 -

12 - 8 - DBSORT Record 06: Parent #1 ID I1 Record where the Parent # 1 ID is located I5 Beginning column number of Parent # 1 ID I5 Ending column number of Parent # 1 ID Record 07: Parent #2 ID I1 Record where the Parent # 2 ID is located I5 Beginning column number of Parent # 2 ID I5 Ending column number of Parent # 2 ID Record 08: Birth Order / Birth Year I1 Record where the Birth Order or Birth Year field is located I5 Beginning column number of Birth Order or Birth Year field I5 Ending column number of Birth Order or Birth Year field Record 09: Birth Month Do not include this record if options BO or BY on record 2 were chosen. Include only if BD option was selected I1 Record where the Birth Month field is located I5 Beginning column number of Birth Month field I5 Ending column number of Birth Month field Record 10: Missing Value Codes A8 Missing value code for Birth Order or Birth Year (Default is blank) A8 Missing value code for Birth Month (Default is blank) Record 11: Month Convention Selection If either option BO or BY was selected on record 2, records 11 through 23 are not needed. If option BD was selected, record 11 is required, and records 12 through 23 may be needed I1 Selection of Month Code convention 0 = Select the default numerical month code option. Records 12 to 23 are not needed in this case. 1 - January; 2 - February; 3 - March; 4 - April; 5 - May; 6 - June; 7 - July; 8 - August; 9 - September; 10 - October; 11 - November;12 - December; 1 = Select the default character month code option. Records 12 to 23 are not needed in this case.

13 DBSORT JAN - January; FEB - February; MAR - March; APR - April; MAY - May; JUN - June; JUL - July; AUG - August; SEP - September; OCT - October; NOV - November; DEC - December; 2 = Select user supplied month code option. Records 12 to 23 are required. The following records are optional because they depend on the month convention selection. If the month convention selection in Record 11 is 2, the user must provide a unique code for each month Record 12: User Specified Code for January A8 User's code for January Record 13: User Specified Code for February A8 User's code for February Record 14: User Specified Code for March A8 User's code for March Record 15: User Specified Code for April A8 User's code for April Record 16: User Specified Code for May A8 User's code for May Record 17: User Specified Code for June A8 User's code for June Record 18: User Specified Code for July A8 User's code for July Record 19: User Specified Code for August A8 User's code for August Record 20: User Specified Code for September A8 User's code for September

14 DBSORT Record 21: User Specified Code for October A8 User's code for October Record 22: User Specified Code for November A8 User's code for November Record 23: User Specified Code for December A8 User's code for December 4.2 Family Data File (Logical Unit 11) The Family Data File should contain the following key information. 1. Family ID: A one to five digit numeric code 2. Individual ID: A one to eight character alphanumeric code 3. Parent # 1 ID: A one to eight character alphanumeric code 4. Parent # 2 ID: A one to eight character alphanumeric code 5. Birth Order or Birth Year: A one to eight character alphanumeric code 6. Birth Month: A one to eight character alphanumeric code Each individual in the family can have up to 6 records and the maximum record length is 132 characters. Anything beyond column 132 will not be read. Missing value codes must be specified in the parameter file. Note: Please see the Release Notes and Installation Guide for more information about FORTRAN format statements.

15 5 Output DBSORT generates two output files. 1. Sorted Family Data File 2. Information File 5.1 Sorted Family Data File (Logical Unit 21) This file contains the sorted family data. The format of the sorted family data is the same as that of the original Family Data File, which can be found on page 11. The individuals with missing birth order or birth year, but who have parents, are put at the bottom of the sorted list within families. The individuals missing both birth information and parents are put at the top of the sorted list within families. 5.2 Information File (Logical Unit 22) This file contains any informational messages obtained while running DBSORT. See the Error Message section for details

16 DBSORT

17 6 Example 6.1 Parameter File (Logical Unit 1) The Parameter File DBSORT.PAR is listed below. DBSORT: EXAMPLE #1 < title BD < sorted by birth date (year & month) 1 < each individual has one record < the family id is located on the st record from column 1 to < missing values are blank 0 < select default numerical month code 6.2 Family Data File (Logical Unit 11) The Sample Data File DBSORT.DAT is listed below N M N N N U Y F N N Y A N M N N U N F N N U Y F N N A N M N N U Y M Y N Y A N F N N N U N F N N N U N F N N U Y M N N N Y F N N N U Y M N N N U Y M Y Y Y A Y M Y Y Y A Y M Y Y Y A Y F Y Y N A Y M A Y M Y M Y Y Y A Y F Y F N N Y A F A M U Y F Y N Y A N M U N M N N N U Y M Y N F U Y F N N N M U Y M Y N Y A N F N N N U Y M N N N U N F U Y M Y M N N U

18 DBSORT N F N N U Y M Y N Y A N F N N U M Y N Y A Y M Y Y Y A Y F N Y F N Y M Y A Y F Y N Y A N M U N M U Y F Y Y F Y N M Y F N N N U Y F Y Y Y A N M N N N U Y F N U Y F Y N Y A Y F Y Y F Y Sorted Family Data File (Logical Unit 21) The Sorted Data File DBSORT.OUT is listed below N M N N U N F N N U N M N N U N F N N N U N F N N U Y F N N Y A N M N N N U Y M Y N Y A N F N N N U Y F N N A Y M Y Y Y A Y F N N N U Y F Y Y N A Y M N N N U Y M Y Y Y A Y M Y Y Y A Y M Y Y Y A Y F N N Y A Y M A Y M Y F Y M N N N F A M U N M U N F U N M U N F U N M N N N U Y F Y N Y A Y F N N Y M Y N Y A Y M N N N U

19 DBSORT N M Y F Y N N A N M U Y F Y N Y A Y F Y N Y A N M N N N U Y F Y N Y A Y F Y Y Y A Y F Y N Y A Y F N N N U Y F Y A Y M Y A Y F Y Y F Y Y F N U Y F Y Y F Y 6.4 Information File (Logical Unit 22) The Information File DBSORT.INF is listed below. S.A.G.E. RELEASE DBSORT DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. ======================================================================== DBSORT: EXAMPLE #1 ======================================================================== %DBSORT-W: The following individuals are missing birth order/birth date information but have parents.! !! FAMILY INDIVIDUAL!! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !

20 DBSORT S.A.G.E. RELEASE DBSORT DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. ======================================================================== DBSORT: EXAMPLE #1 ======================================================================== %DBSORT-W: The following individuals are missing birth order/birth date information and are missing both parents.! !! FAMILY INDIVIDUAL!! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! 3017!! !! !! !! !! !! !! !! !! ! S.A.G.E. RELEASE DBSORT DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. ======================================================================== DBSORT: EXAMPLE #1 ======================================================================== %DBSORT-I: The following individuals are missing birth order/birth date information and are missing one parent.! !! FAMILY INDIVIDUAL!! !! !

21 DBSORT ! ! S.A.G.E. RELEASE DBSORT DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. ======================================================================== DBSORT: EXAMPLE #1 ======================================================================== %DBSORT-I: The following individuals are missing birth order/birth date information and have sibs.! !! FAMILY INDIVIDUAL!! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! !! ! S.A.G.E. RELEASE DBSORT FEB 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. ******************************************** *** An individual with missing *** *** birth order or birth date *** *** but who has sib(s) *** *** may result in an error if used with *** *** the class B or C regression models *** *** in the REGC program. *** *** See documentation for more details. *** *** *** *** *** *** The data should be corrected and *** *** this program must be rerun before *** *** running *** *** FSP and segregation analysis REGC. *** ********************************************

22 DBSORT

23 7 Error Messages DBSORT has an error-checking routine. When an error is detected, DBSORT will identify the type of error and display the error message associated with it. There are three types of errors: 1. %DBSORT-I, Information Messages, 2. %DBSORT-W, Warning Messages, 3. %DBSORT-E, Fatal Error Messages. 7.1 Information Messages %DBSORT-I: The following individuals are missing birth order/birth date information and have sibs. %DBSORT-I: The following individuals are missing birth order/birth date information and are missing one parent. Note: The segregation analysis programs require that either both or neither parents be identified for each individual in the data set. 7.2 Warning Messages %DBSORT-W: Invalid Month Code. Month will be considered as missing. Month Code = (----)for Family (----) Individual (----) This warning occurs when the data is being sorted by birth date and an unrecognized month code is found. The month code will be considered as missing for that particular individual, and the individual will be flagged as having missing birth date information. %DBSORT-W: The following individuals are missing birth order/birth date information but have parents. %DBSORT-W: The following individuals are missing birth order/birth date information and are missing both parents. 7.3 Fatal Error Messages %DBSORT-E: The maximum number of records per individual has been exceeded. This error occurs when the number of records per individual exceeds 6. Since 'NUMBER OF RECORDS PER INDIVIDUAL' is an input parameter, the program terminates before sorting any family

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