Summary: Load marker-locus data Argument: < file name >
This command reads in the marker-locus data (allele frequencies for each genetic marker, frequency and penetrance information for the disease). The format of this file must be identical to the Linkage parameter file (output from the PREPLINK program). See the file linkloci.dat as an example of this file format or consult Linkage documentation for further help.
After 3 header lines (only the number of loci on line 1 and the marker order specified on line 3 are relevant and need to be changed), this file must begin with one (and only one) affectation locus describing the disease allele frequencies and penetrances. Following this should be entered the information for each marker as in the following example:
3 6 # D1S1234 .20 .15 .15 .40 .05 .05
The 3 on the first line is obligatory, followed by the number of alleles for the marker. If desired a '#' followed by the name of the marker may be entered and this name will then appear on the Postscript output of the 'total' command and can be used to enter marker orders using the 'use' command. The second line for each marker simply contains the allele frequencies for alleles 1 through 6 in this case. Map distances (interlocus distances in the marker order specified on line 3) may be entered on the second to last line in this file format.
The 'load markers' command should occur at the beginning of every session as the information loaded here is required by every subsequent step in the analysis process.
See 'help variance components' for information on how phenotype and covariate data should be specified in this file.