RELATIONSHIP TO PROBAND (RELATE)

Transcription

1 RELATIONSHIP TO PROBAND (RELATE) Release 3.1 December 1997

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3 Table of Contents 1 Changes Since Last Release Purpose Limitations Command Line Parameters Theory Relationship to Proband Codes Dummy Variables Input Parameter File (Logical Unit 1) Record 1: Title Record 2: File Information Record 3: Classification Method Classification Records Data Files Family Data File (Logical Unit 11) FSP Pointer Table File (Logical Unit 12) Output Brief Output Pair Frequencies Report (Logical Unit 21) Information File (Logical Unit 22) New Pedigree Data File (Logical Unit 23) Code Totals File (Logical Unit 24) Example Parameter File (Logical Unit 1) The Family Data File (Logical Unit 11) The Pair Frequencies Report (Logical Unit 21) The New Family Data File (Logical Unit 23) Screen Output Information File (Logical Unit 22) Code Totals File (Logical Unit 24) Error Messages Information Messages Warning Messages Error Messages References iii -

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

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7 2 Purpose RELATE is designed to create a set of 0,1 dummy variables that allow each member of a pedigree to be classified on the basis of relationship to a proband. A possible use for such dummy variables is in logistic regression analysis to test hypotheses. It could test whether there is interaction between sex and relationship to the proband, whether the parental effect differs from the child effect, whether the sib effect differs from the parental and child effects, or whether these "familial" effects are significant in the presence of measured environmental variables (George and Elston, 1989). A complete listing of the allowable relationships is given in Section 4.1 of this document. Given a pedigree data file, containing one or more independent pedigrees and one proband per pedigree, RELATE determines the relationship of each individual to the proband, and from this relationship creates the desired dummy variables. RELATE writes a new pedigree data file with an additional record, containing the dummy variables, for each individual

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9 3 Limitations 3.1 Command Line Parameters There are several limitations when analyzing data with this program. The maximum number of probands per pedigree is 1. Each pedigree must have a unique family ID. Also, pedigrees must be ordered such that the family ID's occur in ascending order in the data file. In addition, 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 pedigree MAXIND 5000 Number of pedigrees MAXPED 250 Please see the Release Notes and Installation Guide for details on how to adjust these parameters for your system

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11 4 Theory 4.1 Relationship to Proband Codes Individuals are paired with the proband by the method used in FCOR for generating pairs, and then RELATE gives one of the following codes to each individual: 0 Proband, Female 1 Proband, Male 2 MZ twin, Female 3 MZ twin, Male 4 Mother 5 Father 6 Daughter 7 Son 8 Sib, Female-Sister 9 Sib, Male-Brother 10 DZ twin, Female 11 DZ twin, Male 12 Aunt 13 Uncle 14 Niece 15 Nephew 16 Grandmother 17 Grandfather 18 Granddaughter 19 Grandson 20 Half-Sib, Female 21 Half-Sib, Male 22 Cousin, Female 23 Cousin, Male 24 Great-Aunt 25 Great-Uncle 26 Great-Niece 27 Great-Nephew 28 Half-Aunt 29 Half-Uncle 30 Half-Niece 31 Half-Nephew 32 Great-Grandmother 33 Great-Grandfather 34 Great-Granddaughter 35 Great-Grandson 36 Spouse of Proband, Female 37 Spouse of Proband, Male 38 Unrelated, or 4th degree or more, Female 39 Unrelated, or 4th degree or more, Male 4.2 Dummy Variables RELATE then creates dummy variables on the basis of a user provided classification of the allowable relationships into sets. The creation of dummy variables is most easily explained by an example. Suppose you wish to classify the individuals into six sets based on the degree of the relationship to the proband. Set 1 consists of the proband. Set 2 consists of 1st degree relatives, set 3 consists of 2nd degree relatives, set 4 consists of 3rd degree relatives, set 5 consists of spouses, and set 6 consists of all unrelated individuals and 4th degree or greater relatives. Note: This is an example and is not intended to be used as a model of desirable sets. The actual sets to be used are specified in the RELATE parameter file. Therefore, using the relationship to proband codes, Section 4.1, the sets will look like this: - 7 -

12 - 8 - RELATE Relationship to Proband Codes Set 1: 0,1 Set 2: 2,3,4,5,6,7,8,9,10,11 Set 3: 12,13,14,15,16,17,18,19,20,21 Set 4: 22,23,24,25,26,27,28,29,30,31,32,33,34,35 Set 5: 36,37 Set 6: 38,39 This classification is used to create six variables (V1, V2, V3, V4, V5, V6) for every pedigree member, each of which has the value 0 or 1, as indicated in the following table: VARIABLE V1 V2 V3 V4 V5 V6 Proband Relationship to Proband Spouse Unrelated For example, a 1st degree relative, i.e. a member of set 2, will have the variable values V1 = 0, V2 = 1, V3 = 0, V4 = 0, V5 = 0, and V6 = 0. The dummy variables for every member of set 2 would be RELATE writes the new dummy variables created for each individual to the new pedigree data file on an additional record which follows the original set of data records for that individual.

13 5 Input The following set of records is used to determine the type of sample and analysis to be performed: 1. Parameter File S used to configure the program execution through parameter records. 2. Classification Records 3. Family Data File - the raw data file containing the Study ID, Family ID, Individual ID, Parent IDs, Sex, and individual data. 4. FSP Pointer Table File (.lnk) - contains the pointer table and is produced by the program FSP. 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. 5.1 Parameter File (Logical Unit 1) The RELATE parameter file must contain records 1 and 2. Record 3 is optional. If Record 3 is used and the value in column 1 is 0, classification records must follow Record Record 1: Title Column Format Description A80 Title of run Record 2: File Information Column Format Description I5 Number of records per individual in the Family Data File; (Default is 1) Record 3: Classification Method Record 3 is optional. If you choose to omit Record 3, RELATE will use classification method 1 and will print the warning message: WARN -> NO CLASSIFICATION METHOD SELECTED. USING METHOD 1. Column Format Description I5 Method used to classify the relationship to proband codes; (Default is 1) 0 = The user will specify the classification method using the classification records. 1 = Codes will be classified separately. (A set for each code) 2 = Classified by degree of relationship 3 = Classified by degree of relationship and by sex 4 = Classified by degree, 1st degree split into parent-child, and sib groups 5 = Classified by degree, 1st degree split into parent, child, and sib groups - 9 -

14 RELATE The previous descriptions are approximate; below is a more precise description of the classification methods available. Method Description 0 You specify the method by adding classification records as indicated below. 1 Each code is in a separate set. 2 By degree of relationship set 1: 0, 1, 2, 3 set 2: 4-11 set 3: set 4: set 5: 36, 37 set 6: 38, 39 3 By degree of relationship set 1: 0, 2 and sex set 2: 1, 3 set 3: 4, 6, 8, 10 set 4: 5, 7, 9, 11 set 5: 12, 14, 16, 18, 20 set 6: 13, 15, 17, 19, 21 set 7: 22, 24, 26, 28, 30, 32, 34 set 8: 23, 25, 27, 29, 31, 33, 35 set 9: 36 set 10: 37 set 11: 38 set 12: 39 4 Classified by degree, 1 st set 1: 0-3 degree split into parent- set 2: 4-7 child, and sib groups set 3: 8-11 set 4: set 5: set 6: 36, 37 set 7: 38, 39 5 Classified by degree, 1 st set 1: 0-3 degree split into parent, set 2: 4, 5 child, and sib groups. set 3: 6, 7 set 4: 8-11 set 5: set 6: set 7: 36, 37 set 8: 38, Classification Records By using classification records, you may specify your own classification method (method 0). In order to use them, you must include Record 3 above with a 0 in column 5. Each classification record must follow several syntax rules. Each record must be terminated by a semicolon (;). The numbers in each record, representing the relationship to proband codes, must be separated by commas (,) with no spaces either before or after the numbers. The maximum record length is 132 characters.

15 RELATE The first classification record contains the number of sets; for example, n. This record will be followed by n records, each containing the relationship to proband codes that belong to a particular set. Each relationship to proband code must be used once and only once in the n classification records. There will be n + 1 classification records. RELATE performs a syntax check on the classification records and will print a warning or error message if the records violate any of the syntax rules. The classification records must follow this format: Classification Records Example record 1: number of sets, n 5; record 2: codes that are members of set 1 0,1,2,3,4; record 1 + n: codes that are members of set n 38,39; Valid codes are 0 through 39. See Section Data Files Family Data File (Logical Unit 11) This is the original or raw data file FSP Pointer Table File (Logical Unit 12) Prior to running the program RELATE, you will need to run FSP, the pedigree structure program, to create an FSP pointer table file. You must select certain options in the FSP parameter file to produce this file. Record 2 of the FSP parameter file must have a 1 in column 5 to create the FSP pointer table file and a 1 in column 20 to include a proband variable. Records 4 and 5 must be included in order to include a code for proband status for each individual and its location in the original data file. Before running RELATE, you should also look in the information file produced by FSP for information about the pedigree(s) to see if any errors are present in your data.

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17 6 Output 6.1 Brief Output RELATE writes selected informational, warning, and error messages to the screen. 6.2 Pair Frequencies Report (Logical Unit 21) For each pedigree, the pair frequencies report shows the total number of proband-nonproband pairs (i.e., the number of pedigree members minus one), the number of proband-nonproband pairs broken down by main types of relationship, and the number of proband-nonproband pairs broken down by sex-specific relationship subtypes. In addition, the report also shows these numbers totaled over all pedigrees. This is written to logical unit Information File (Logical Unit 22) As the program RELATE runs, it prints various messages to inform you of its progress and of any warning or error conditions. If RELATE is run interactively, it will print informational and warning messages on the screen. If RELATE is run as a batch job, it will print these messages in your log file. In addition, RELATE will print all informational, warning, and error messages in the information file. Informational messages begin with the prefix INF ->, warning messages begin with the prefix WARN ->, and error messages begin with the prefix ERROR ->. This is written to logical unit New Pedigree Data File (Logical Unit 23) For each individual, RELATE copies the original set of data records from the original pedigree data file into the New Pedigree Data File, followed by a new record containing the n dummy variables created by RELATE, where n equals the number of classification sets. RELATE writes these n dummy variables using the format 40(I1,1X). This is written to logical unit Code Totals File (Logical Unit 24) For each pedigree, the code totals file shows the total number of members with each code and the total number of members in each set. In addition, this file also shows the totals over all pedigrees. This is written to logical unit

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19 7 Example In this example, the pedigree data file contains two pedigrees with three records per individual. The proband code is in column 37 of the first record of each individual. The sex codes are "1" for male and "2" for female. This example will group the relationship to proband codes into six sets. Set 1 will consist of the codes 0 and 1. Set 2 will consist of codes Set 3 will consist of codes Set 4 will consist of codes Set 5 will consist of codes 36 and 37, and set 6 will consist of codes 38 and 39. Listings of the following files are provided for this example: + - RELATE Parameter File Input 1. - A segment of the Family Data File + - Screen output * - A segment of the Pair Frequencies Report Output 1 - Information File * - A segment of the New Family Data File. - Code totals file 7.1 Parameter File (Logical Unit 1) The Parameter File RELATE.PAR is listed below. RELATE EXAMPLE ; 0,1; 2,3,4,5,6,7,8,9,10,11; 12,13,14,15,16,17,18,19,20,21; 22,23,24,25,26,27,28,29,30,31,32,33,34,35; 36,37; 38,39; 7.2 The Family Data File (Logical Unit 11) A segment of the Family Data File RELATE.DAT is listed below B M B F M F M

20 RELATE B M B F B M B F M F B M B F The Pair Frequencies Report (Logical Unit 21) A segment of the Pair Frequencies Report RELATE.PRF is listed below. S.A.G.E. RELEASE RELATE DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. PAIR FREQUENCIES REPORT: RELATE EXAMPLE 1 **** PEDIGREE NUMBER: **** Pairs Found TOTALS Broken down by MAINTYPE. Types with zero pairs not reported. Pairs Found PARENTAL... 2 SIBLING... 5 GRANDPARENT... 4 AVUNCULAR... 3 Broken down by SUBTYPE. Types with zero pairs not reported. Pairs Found Mother: Son... 1 Father: Son... 1 Brother: Brother... 5 Maternal Grandmother: Grandson... 1 Maternal Grandfather: Grandson... 1 Paternal Grandmother: Grandson... 1 Paternal Grandfather: Grandson... 1 Paternal Uncle: Nephew

21 RELATE S.A.G.E. RELEASE RELATE DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. PAIR FREQUENCIES REPORT: RELATE EXAMPLE 1 **** TOTAL PAIRS OVER ALL PEDIGREES **** Pairs Found TOTALS Broken down by MAINTYPE. Types with zero pairs not reported. Pairs Found PARENTAL... 4 SIBLING... 8 GRANDPARENT... 8 AVUNCULAR... 7 Broken down by SUBTYPE. Types with zero pairs not reported. Pairs Found Mother: Son... 2 Father: Son... 2 Brother: Brother... 8 Maternal Grandmother: Grandson... 2 Maternal Grandfather: Grandson... 2 Paternal Grandmother: Grandson... 2 Paternal Grandfather: Grandson... 2 Paternal Uncle: Niece... 1 Paternal Uncle: Nephew The New Family Data File (Logical Unit 23) A segment of the New Family Data File RELATE.NEW is listed below B M B F M F M F M

22 RELATE B F M F B M B F Screen Output INF -> RELATE IS RUNNING... INF -> FINDING PAIRS FOR PEDIGREE INF -> FINDING PAIRS FOR PEDIGREE INF -> BEGINNING ASSIGNMENT OF DUMMY VARIABLES. INF -> PEDIGREE UNUSED CODE(S). INF -> PEDIGREE EMPTY CLASSIFICATION SET(S). INF -> PEDIGREE UNUSED CODE(S). INF -> PEDIGREE EMPTY CLASSIFICATION SET(S). INF -> ASSIGNMENT OF DUMMY VARIABLES COMPLETED. 7.6 Information File (Logical Unit 22) The Information File RELATE.INF is listed below. S.A.G.E. RELEASE RELATE DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. **** RELATE INFORMATION FILE **** %RELATE-I: RELATE IS RUNNING... %RELATE-I: FINDING PAIRS FOR PEDIGREE %RELATE-I: FINDING PAIRS FOR PEDIGREE %RELATE-I: BEGINNING ASSIGNMENT OF DUMMY VARIABLES. %RELATE-I: PEDIGREE UNUSED CODE(S). %RELATE-I: CODE 0 NOT USED. Proband, Female %RELATE-I: CODE 2 NOT USED. MZ twin, Female %RELATE-I: CODE 3 NOT USED. MZ twin, Male %RELATE-I: CODE 6 NOT USED. Daughter %RELATE-I: CODE 7 NOT USED. Son %RELATE-I: CODE 8 NOT USED. Sib, Female-Sister %RELATE-I: CODE 10 NOT USED. DZ twin, Female %RELATE-I: CODE 11 NOT USED. DZ twin, Male %RELATE-I: CODE 12 NOT USED. Aunt %RELATE-I: CODE 13 NOT USED. Uncle %RELATE-I: CODE 14 NOT USED. Niece %RELATE-I: CODE 18 NOT USED. Granddaughter %RELATE-I: CODE 19 NOT USED. Grandson %RELATE-I: CODE 20 NOT USED. Half-Sib, Female %RELATE-I: CODE 21 NOT USED. Half-Sib, Male

23 %RELATE-I: CODE 22 NOT USED. Cousin, Female %RELATE-I: CODE 23 NOT USED. Cousin, Male %RELATE-I: CODE 24 NOT USED. Great-Aunt %RELATE-I: CODE 25 NOT USED. Great-Uncle %RELATE-I: CODE 26 NOT USED. Great-Niece %RELATE-I: CODE 27 NOT USED. Great-Nephew %RELATE-I: CODE 28 NOT USED. Half-Aunt %RELATE-I: CODE 29 NOT USED. Half-Uncle %RELATE-I: CODE 30 NOT USED. Half-Niece %RELATE-I: CODE 31 NOT USED. Half-Nephew %RELATE-I: CODE 32 NOT USED. Great-Grandmother %RELATE-I: CODE 33 NOT USED. Great-Grandfather %RELATE-I: CODE 34 NOT USED. Great-Granddaughter %RELATE-I: CODE 35 NOT USED. Great-Grandson %RELATE-I: CODE 36 NOT USED. Spouse of Proband, Female %RELATE-I: CODE 37 NOT USED. Spouse of Proband, Male %RELATE-I: CODE 39 NOT USED. Unrelated and 4th degree or more, Male %RELATE-I: PEDIGREE EMPTY CLASSIFICATION SET(S). %RELATE-I: CLASSIFICATION SET 4 HAS NO MEMBERS. %RELATE-I: CLASSIFICATION SET 5 HAS NO MEMBERS. %RELATE-I: PEDIGREE UNUSED CODE(S). %RELATE-I: CODE 0 NOT USED. Proband, Female %RELATE-I: CODE 2 NOT USED. MZ twin, Female %RELATE-I: CODE 3 NOT USED. MZ twin, Male %RELATE-I: CODE 6 NOT USED. Daughter %RELATE-I: CODE 7 NOT USED. Son %RELATE-I: CODE 8 NOT USED. Sib, Female-Sister %RELATE-I: CODE 10 NOT USED. DZ twin, Female %RELATE-I: CODE 11 NOT USED. DZ twin, Male %RELATE-I: CODE 12 NOT USED. Aunt %RELATE-I: CODE 13 NOT USED. Uncle %RELATE-I: CODE 18 NOT USED. Granddaughter %RELATE-I: CODE 19 NOT USED. Grandson %RELATE-I: CODE 20 NOT USED. Half-Sib, Female %RELATE-I: CODE 21 NOT USED. Half-Sib, Male %RELATE-I: CODE 22 NOT USED. Cousin, Female %RELATE-I: CODE 23 NOT USED. Cousin, Male %RELATE-I: CODE 24 NOT USED. Great-Aunt %RELATE-I: CODE 25 NOT USED. Great-Uncle %RELATE-I: CODE 26 NOT USED. Great-Niece %RELATE-I: CODE 27 NOT USED. Great-Nephew %RELATE-I: CODE 28 NOT USED. Half-Aunt %RELATE-I: CODE 29 NOT USED. Half-Uncle %RELATE-I: CODE 30 NOT USED. Half-Niece %RELATE-I: CODE 31 NOT USED. Half-Nephew %RELATE-I: CODE 32 NOT USED. Great-Grandmother %RELATE-I: CODE 33 NOT USED. Great-Grandfather %RELATE-I: CODE 34 NOT USED. Great-Granddaughter %RELATE-I: CODE 35 NOT USED. Great-Grandson %RELATE-I: CODE 36 NOT USED. Spouse of Proband, Female %RELATE-I: CODE 37 NOT USED. Spouse of Proband, Male %RELATE-I: CODE 39 NOT USED. Unrelated and 4th degree or more, Male %RELATE-I: PEDIGREE EMPTY CLASSIFICATION SET(S). %RELATE-I: CLASSIFICATION SET 4 HAS NO MEMBERS. %RELATE-I: CLASSIFICATION SET 5 HAS NO MEMBERS. %RELATE-I: ASSIGNMENT OF DUMMY VARIABLES COMPLETED. 7.7 Code Totals File (Logical 24) The Code Totals File RELATE.TOT is listed below. S.A.G.E. RELEASE RELATE DECEMBER 1997 COPYRIGHT (C) 1997 CASE WESTERN RESERVE UNIVERSITY. RELATE

24 RELATE **** RELATE CODE TOTALS FILE **** PEDIGREE NUMBER OF INDIVIDUALS WITH EACH CODE. NUMBER OF INDIVIDUALS IN EACH SET. CODE # OF INDIVIDUALS RELATIONSHIP TO PROBAND SET # OF INDIVIDUALS 1 1 Proband, Male Mother Father Sib, Male-Brother Nephew 16 2 Grandmother 17 2 Grandfather 38 5 Unrelated and 4th degree or more, Female TOTAL 20 TOTAL 20 PEDIGREE NUMBER OF INDIVIDUALS WITH EACH CODE. NUMBER OF INDIVIDUALS IN EACH SET. CODE # OF INDIVIDUALS RELATIONSHIP TO PROBAND SET # OF INDIVIDUALS 1 1 Proband, Male Mother Father Sib, Male-Brother Niece 15 3 Nephew 16 2 Grandmother 17 2 Grandfather 38 3 Unrelated and 4th degree or more, Female TOTAL 17 TOTAL 17 FINAL TOTALS. NUMBER OF INDIVIDUALS WITH EACH CODE. NUMBER OF INDIVIDUALS IN EACH SET. CODE # OF INDIVIDUALS RELATIONSHIP TO PROBAND SET # OF INDIVIDUALS 1 2 Proband, Male Mother Father Sib, Male-Brother Niece 15 6 Nephew 16 4 Grandmother 17 4 Grandfather 38 8 Unrelated and 4th degree or more, Female TOTAL 37 TOTAL 37

25 8 Error Messages RELATE has an error checking routine. When an error is detected during the analysis, RELATE will identify the type of error and display the error message associated with it. There are three types of errors: %RELATE-I, Information Messages %RELATE-W, Warning Messages %RELATE-E, Fatal Error Messages Only a Fatal Error will cause the program to terminate. 8.1 Information Messages RELATE prints informational messages to inform you of its progress and termination. For example, if the program had run and terminated without an error it would print messages similar to the following: %RELATE-I: RELATE IS RUNNING... %RELATE-I: FINDING PAIRS FOR PEDIGREE x. %RELATE-I: BEGINNING ASSIGNMENT OF DUMMY VARIABLES. %RELATE-I: ASSIGNMENT OF DUMMY VARIABLES COMPLETED. RELATE prints the following messages to provide information about how the chosen classification method performed. %RELATE-I: FINDING PAIRS FOR PEDIGREE x. RELATE is finding proband-nonproband pairs for pedigree x. RELATE will print this message once for each pedigree in the raw data file. %RELATE-I: PEDIGREE x. UNUSED CODE(S). RELATE did not assign one or more of the relationship to proband codes to individuals in pedigree x. Check the information file to see which codes were not used. %RELATE-I: CODE y NOT USED. There are no individuals in the pedigree(s) with the relationship to proband code y. This message appears only in the information file. %RELATE-I: PEDIGREE x. EMPTY CLASSIFICATION SET(S). RELATE did not place any individuals in pedigree x in one or more of the classification sets. Check the information file to see which sets were empty. %RELATE-I: CLASSIFICATION SET y HAS NO MEMBERS. There are no individuals in the pedigree(s) in classification set y. This message appears only in the information file

26 RELATE 8.2 Warning Messages RELATE may print any of the following warning messages in the information file and on the screen (or in your log file) to indicate action it has taken on certain classification record syntax errors. The program will continue to execute after printing any of these messages. Note: Warning messages indicate that the program is making assumptions about your classification records. These assumptions may or may not lead to the results you intend. If the program prints any warning message(s), you should correct the classification records (Section 5.1.4) if necessary. %RELATE-W: NO SEMICOLON. ASSUMING SEMICOLON AT END. A classification record is not terminated by a semicolon (;). The program assumes that a semicolon is at the end of the record. The program prints the classification record following the message. %RELATE-W: MULTIPLE SEMICOLONS. ASSUMING 1ST SEMICOLON IS END. A classification record contains multiple semicolons. The program ignores the portion of the record to the right of the left-most semicolon. The program prints the classification record following the message. %RELATE-W: ILLEGAL CODE x IN SET y IGNORED. A classification record contains an invalid relationship to proband code. The program will ignore the invalid code x. The code occurred in set y. Set y is record (y + 1) of the classification records. %RELATE-W: INVALID CLASSIFICATION METHOD y. USING METHOD 1. Record 3 contains an invalid method. The program will use the default method 1. %RELATE-W: NO CLASSIFICATION METHOD SELECTED. USING METHOD 1. Record 3 is missing from the RELATE parameter file. The program will use the default method 1. %RELATE-W: INVALID NUMBER OF RECORDS PER INDIVIDUAL x. USING DEFAULT OF 1. Record 2 contains a non-integer value for the number of records per individual in the raw data file. The program will use a default value of Error Messages Several conditions will cause the program to stop before completion. If any of these fatal errors occur, RELATE will print one or more of the following messages in the information file and on the screen. %RELATE-E: RELATE TERMINATING BECAUSE OF ERROR(S). This message indicates that RELATE stopped because of errors before it finished processing the data.

27 %RELATE-E: INVALID SEX CODE x IN PEDIGREE y INDIVIDUAL z. RELATE Individual z in pedigree y has an invalid sex code. The invalid sex code is x. This message usually indicates that the individual has a missing sex code. It can occur even if sex is not required for the chosen method of classification. %RELATE-E: PEDIGREE ID IS NOT UNIQUE: x The pedigree ID x is used by more than one pedigree in the data file. Pedigree IDs must be unique. %RELATE-E: PEDIGREE IDS NOT IN ASCENDING ORDER. The pedigrees do not occur in the data file such that the pedigree IDs are in ascending order. The pedigrees must be ordered such that the pedigree IDs occur in ascending order. %RELATE-E: TOO MANY PEDIGREES IN DATA FILE. MAXIMUM # ALLOWED IS x. The data file contains too many pedigrees. The maximum number of pedigrees allowed in a data file is x. %RELATE-E: PEDIGREE x HAS y PROBANDS. Pedigree x has y probands. Each pedigree in the pedigree data file must have exactly one proband. %RELATE-E: CODE x BELONGS TO y CLASSIFICATION SETS. Code x belongs to y number of classification sets. Each code must belong to exactly one classification set. %RELATE-E: CODES MUST BELONG TO EXACTLY ONE CLASSIFICATION SET. This message will follow one or more cases of the previous message. %RELATE-E: MISSING CLASSIFICATION RECORD(S). One or more classification records are missing. %RELATE-E: UNEXPECTED END-OF-FILE, UNIT NUMBER x. The end of the file assigned to unit x was reached unexpectedly.

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29 References George VT, Elston RC. [1989]: "Biostatistical methods for the familial study of cancer", in Genetic Epidemiology of Cancer (Chapter 2) edited by Lynch and Hirayama, CRC Press, Inc