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renumf90 |
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How do
OPTIONs work?
DATAFILE f1 # data file name TRAITS t1 t2 t3 ... # positions of traits in data file FIELDS_PASSED TO OUTPUT p1 p2 .. pm # positions that are not renumbered WEIGHT(S) w # position of weight - fraction to the residual variance RESIDUAL_VARIANCE R # matrix of residual (co)variances EFFECT e1 e2 e3 ... type form # e1 e2 e3 ... = position of this effect for each trait # type = 'cross' for crossclassified or 'cov' for covariables # form = 'alpha' for alphanumeric or 'numer' for numeric EFFECT d1 d2 d3 ... cov; # d1 d2 d3 ... = positions of covariables nested in the following crossclassified effects NESTED e1 e2 e3 ... form # e1 e2 e3 ... = positions of crossclassified effects nested # form = 'alpha' for alphanumeric or 'numer' for numeric RANDOM random_type # 'diagonal', 'sire' or 'animal' for random effect OPTIONAL o1 o2 o3 ... # 'pe' for permanent environment, 'mat' for maternal, and 'mpe' for maternal permanent environment FILE fped # pedigree file name an s d alt_dam yob # positions of animal, sire, dam, alternate dam (recipient dam), and year of birth in pedigree file (default 1 2 3 0 0). SNP_FILE fsnp # fsnp specifies files with ID and SNP information; if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will include the genomic information; file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and include digits 0, 1, 2 and 5; ID and SNP info need to be separated by at leats one space; see info for program PreGSf90. PED_DEPTH p # depth of pedigree search (default 3); all pedigrees are loaded if p=0. GEN_INT min avg max # minimum, average and maximum generation interval; applicable only if year of birth present in pedigree file; minimum and maximum used for pedigree checks; average used to predict year of birth of parent with missing pedigree. REC_SEX sex # if only one sex has records, specifies which parent it is; used for pedigree checks. UPG_TYPE t # 'yob' = based on year of birth; if 'in_pedigrees', the value of a missing parent should be -x, where x is UPG number from 1 that this missing parent should be allocated to; in this option, all known parents should have pedigree lines, i.e., each parent field should contain either the ID of a real parent, or a negative UPG number. if it is 'internal', allocation is by a user-written function custom_upg (year_of_birth,sex,ID, parent_code). (CO)VARIANCES g # (co)variances for animal effects or animal + maternal effects (CO)VARIANCES_PE gpe # (co)variances for the PE effect (CO)VARIANCES_MPE gmpe # (co)variances for the MPE effect What is the format of the pedigree file? The additive pedigree file renadd** has the following structure: 1) animal number (from 1) 2) parent 1 number or unknown parent group number for parent 1 3) parent 2 number or unknown parent group number for parent 2 4) 3 minus number of known parents 5) known or estimated year of birth (0 if not provided) 6) number of known parents 7) number of records 8) number of progenies as parent 1 9) number of progenies as parent 2 10) original animal id Can we change the maximum size of character fields? OPTION alpha_size nn # new size (default 20 characters). How can we specify interactions? Combining fields or interactions Several fields in the data file can be combined into one using a COMBINE keyword. COMBINE a b c .... Keywords COMBINE need to be on top of the parameter file, but possibly after comments. For example: COMBINE 7 2 3 4 combines content of fields 2 3 4 into field 7; the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces). The combined fields can be treated as "numeric" with the total length is < 9 or "alpha". Need more examples? |
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