Forms linkage groups using marker data from experimental populations (J. Jansen, J.T.N.M. Thissen & M.P. Boer).
|What to print (
||Type of population (
||Whether to increase the number of recombinations by 0.5 recombination per informative meiosis for each missing marker score (
||Threshold for the recombination frequency at which markers are said to be linked; default 0.2|
||Marker scores for each marker; must be set|
||Saves the linkage groups of the markers|
||Names of the markers; must be set|
||Marker scores of the parents; must be set|
||Saves the marker scores factors according to the
||Saves the sorted linkage groups|
||Saves the names of the markers according to the
||Saves the parent information according to the
QLINKAGEGROUPS forms linkage groups of markers using marker data from experimental populations. The marker scores of the genotypes are supplied in a pointer by the
MKSCORES parameter. This contains a set of factors (with levels all in the same order), each one with the data for one of the markers. The names of the markers must be supplied, in a text, using the
MKNAMES parameter. The marker scores of the parents must be supplied using the
QLINKAGEGROUPS calculates the recombination frequencies from the marker scores. The calculation depends on the population type, which must be specified by the
POPULATIONTYPE option. You can set option
USEPENALTY=yes to impose a penalty for missing data: the number of recombinations is then increased by 0.5 recombination per informative meiosis for each missing marker score.
Next the recombination frequencies are used to determine whether markers are linked, using a threshold provided by the
THRESHOLD option; this can be either a scalar or a variate (default 0.2). If
POPULATIONTYPE=CP, parent information must be supplied by the
PARENTS parameter. The linkage groups can be saved using the
CHROMOSOMES parameter. If
THRESHOLD is a scalar, this saves a factor, otherwise it saves a pointer of factors (one for each value in the variate).
The parameters beginning with the prefix
S can be used to save information, sorted into ascending order according to the levels of the
CHROMOSOMES factor(s). The
SCHROMOSOMES parameter saves either a single factor or a pointer of factors, according to whether
THRESHOLD is a scalar or a variate. These contain all values of the linkage group designated
'1', followed by the linkage group designated
'2', and so on. Similarly the
SMKNAMES parameter saves either a text or a pointer of texts. These contain the names of the markers, starting with those of the first
CHROMOSOMES level, then the second level, and so on. They are sorted alphabetically within each
CHROMOSOMES level. The marker scores and parent information are saved by the
SPARENTS parameters, respectively. These save pointers with either one or two levels of suffixes, according to whether
THRESHOLD is a scalar or a variate. The information that they contain is sorted according to the
summary setting prints the number of markers in each linkage group.
The recombination frequencies are calculated by the
QRECOMBINATIONS procedure, using the two-point method. Linkage groups are formed using depth-first search from a symmetric matrix of links.
Restrictions are not allowed.
Cormen T.H., Leiserson, C.E., Rivest R.L. & Stein, C. (2001). Introduction to Algorithms, 2nd edition. MIT Press and McGraw-Hill, Cambridge, Massachusetts.
CAPTION 'QLINKAGEGROUPS example'; STYLE=meta QIMPORT [POPULATION=F2] '%GENDIR%/Examples/F2maize_geno.txt';\ MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents QLINKAGEGROUPS [PRINT=summary; POPULATION=F2;\ THRESHOLD=!(0.15,0.20,0.25,0.30)] \ MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\ CHROMOSOMES=chromosomes PRINT mknames,chromosomes; DECIMALS=0 QIMPORT [POPULATION=CP] '%GENDIR%/Examples/CPapple_GENO.txt'; \ MKSCORES=mkscores ; MKNAMES=mknames; PARENTS=parents QLINKAGEGROUPS [PRINT=summary; POPULATION=CP;\ THRESHOLD=!(0.15,0.20,0.25,0.30)] \ MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\ CHROMOSOMES=chr PRINT mknames, chr; DECIMALS=0