Depending on the model of analysis chosen, additional input files may be required.
For each random effect fitted for which the covariance option GIN (see 4.9.4) has been specified, WOMBAT expects a file set up by the user which contains the inverse of the matrix (such as relationship or correlation matrix) which determines the ‘structure’ of the covariance matrix for the random effect. The following rules apply :
Here ‘row’ and ‘column’ numbers should range from to , where is
the number of levels for the random effect.
Only the elements of the lower triangle of the inverse should be given and given ‘row-wise’, i.e. WOMBAT expects a ’column’ number which is less than or equal to the ‘row’ number.
By default, WOMBAT determines the number of levels for a random effect with covariance option GIN from the data, renumbering them in ascending numerical order. In some cases, however, we might want to fit additional levels, not represented in the data. A typical example is am additional genetic effect, which can have levels not in the data linked to those in the data through covariances arising from co-ancestry.
If WOMBAT encounters row or column numbers greater than the number of random effect levels found in the data, it will take the following action:
For an analysis using the run option --s1step where the user supplied matrix represents the inverse of the joint relationship matrix between genotyped and non-genotyped animals, the .codes file is required to have a third column with the code 1 for non-genotyped and 2 for genotyped individuals.
If a regression on a user- defined set of basis functions has been chosen in the model of analysis by specifying the code USR for a covariable (or ‘control’ variable in a RR analysis), file(s) specifying the functions need to be supplied.
The form required for these files is:
EXAMPLE: If the model of analysis includes the effect age and the maximum number of regression coefficients for age is 7, the corresponding input file expected is age_USR7.baf
N.B.: The file name does not include a trait number.
This implies, that for multivariate analyses the same basis function is assumed to be used for a particular covariable across all traits. The only differentiation allowed is that the number of regression coefficients may be different (i.e. that a subset of coefficients may be fitted for some traits); in this case, the file supplied must correspond to the largest number of coefficients specified.
EXAMPLE: Assume the covariable has possible values of 1, 3, 5, 7 and 9, and that we want to fit a cubic regression on ’ordinary’ polynomials, including the intercept. In this case, WOMBAT would expect to find a file with 5 rows (corresponding to the 5 values of the covariable) and 4 columns (corresponding to the 4 regression coefficients, i.e. intercept, linear, quadratic and cubic):
Note that there is no leading column with the value of the covariable (you can add it as the last column which is ignored by WOMBAT, if you wish) – the association between value of covariable and user defined function is made through the order of records.
For an analysis using the run option --snap, an additional input file is required which supplies the counts for the reference allele for each QTL or SNP to be considered. This has the default name QTLAllels.dat or QTLAllelsR.dat, depending whether integer or or real input is chosen. If both exist in the working directory, WOMBAT will utilize the former and ignore the latter.
For a run with option --itsum or --pool, WOMBAT expects a number of files with results from part analyses as input. Typically, these have been generated by WOMBAT when carrying out these analyses; see 7.2.6 for further details.
For run option --pool, results can be given in a single file instead. For each part analysis, this should contain the following information:
WOMBAT will check for existence of other files with default names in the working directory and, if they exist, acquire information from them.
This file can be used as an alternative to the command line to specify run options
It must have one line for each run option specified, e.g.
to specify a run with verbose output using the EM-algorithm.
In some cases, WOMBAT expects input files with specific names. If files with different default names have the same content, duplication can be avoided by setting up a file FileSynonyms to ‘map’ specific files to a single input file. This file should contain one line for each input file to be ‘mapped’ to another file. Each line should give two file names (space separated) :
[Not yet implemented !]
To simulate data, WOMBAT requires two integer values to initialise the random number generator. If the file RandomSeeds exists, it will attempt to read these values from it. Both numbers can be specified on the same or different lines. If the file does not exist in the working directory, or if an error reading is encountered, initial numbers are instead derived from the date and time of day.
WOMBAT writes out such file in each simulation run, i.e. if RandomSeeds exists, it is overwritten with a new pair of numbers !
For a run with option --itsum, WOMBAT expects to read a list of names of files with results from subset analyses in a file with the standard name SubSetsList. This has generated by WOMBAT (see 7.3.9) if the part analyses have been carried out using WOMBAT, but may need editing. In particular, if a weighted summation is required, the default weights of ‘1.000’, need to be replaced ‘manually’ by appropriate values, selected by the user !
For penalty options COVARM and CORREL a file with this name must be supplied which gives the shrinkage target. This must be a positive definite matrix. The file should be a plain text file and contain the elements of the upper triangle of the matrix. It is read in ‘free’ format, i.e. variable numbers of elements per line are allowed.
A run with the option --valid expects to read sets of estimates from a file with this name. This is generated by WOMBAT when penalized estimation is specified, but can be edited to suit or generated by other means. For each tuning factor, it should contain: