Constructs genetic linkage maps using marker data from experimental populations (J. Jansen, J.T.N.M. Thissen & M.P. Boer).
Options
PRINT = string token |
What to print (map, monitoring, summary); default summ |
|---|---|
PLOT = string token |
What to plot (frequencies, map); default map |
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, CP); must be set |
USEPENALTY = string token |
Whether to increase the number of recombinations by 0.5 recombination per informative meiosis for each missing marker score (yes, no); default no |
SPATIALMETHOD = string token |
Which method to use for clustering (sampling, optimization, none); default opti for population CP, samp otherwise |
NGROUPS = scalar |
Number of groups for clustering; default 10 |
MAPCHROMOSOMES = variate, text or scalar |
Allows a subset of chromosomes to be mapped; default * i.e. all the chromosomes |
LINKAGEPHASES = string token |
Controls estimation of linkage phases for population type CP (estimate, omit); default esti |
TITLE = text |
General title for the graph |
OUTFILENAME = text |
Name (without extension) of the Flapjack files to be created |
Parameters
MKSCORES = pointers |
Marker scores for each marker; must be set |
|---|---|
CHROMOSOMES = factors |
Factor defining the linkage groups |
POSITIONS = variates |
Saves the positions of markers |
MKNAMES = texts |
Names of the markers; must be set |
IDMGENOTYPES = texts |
Names of the genotypes |
PARENTS = pointers |
Marker scores of the parents; must be set |
IDPARENTS = texts |
Labels to identify the parents |
SMKSCORES = pointers |
Saves the scores of the markers, sorted according to the markers in the SCHROMOSOMES factor (if CHROMOSOMES is set) and the SPOSITIONS variate |
SCHROMOSOMES = factors |
Saves the sorted linkage groups |
SPOSITIONS = variates |
Saves the sorted positions of markers (within the sorted linkage groups if CHROMOSOMES is set) |
SMKNAMES = texts |
Saves the names of the markers, sorted according to the SCHROMOSOMES factor (if CHROMOSOMES is set) and the SPOSITIONS variate |
SPARENTS = pointers |
Saves the marker scores of the parents, sorted according to the markers in the SCHROMOSOMES factor (if CHROMOSOMES is set) and the SPOSITIONS variate |
SEED = scalars |
Seed for the random numbers used for spatial sampling; default 0 |
Description
QMAP calculates the order and positions of the markers per chromosome or linkage group. 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. If the CHROMOSOMES parameter is set, the calculation of the positions is done separately for each of its levels (otherwise the markers are assumed to belong to the same linkage group). The MAPCHROMOSOMES option can be set to specify that the calculations are done only for only a subset of the CHROMOSOMES. The names of the markers must be supplied (in a text) using the MKNAMES parameter, and the names of the genotypes must be supplied (also in a text) using the IDMGENOTYPES parameter.
The POPULATIONTYPE option must be set to specify the type of population from which the marker scores have been obtained. The marker scores of the parents must be supplied using the PARENTS parameter. The names of the parents can be supplied using the IDPARENTS parameter. For population types DH1, BC1, F2 and RIL the calculation of the positions starts with the calculation of the number of recombinations per linkage group. The USEPENALTY option controls whether the number of recombinations is increased by 0.5 recombination per informative meiosis for each missing marker score.
This is followed by a spatial clustering. The SPATIALMETHOD option specifies whether this uses random sampling or spatial optimization, or you can set SPATIALMETHOD=none to suppress the clustering. The SEED option specifies the seed for the random numbers used for random sampling; the default of zero selects the seed at random, using the computer clock, or continues the existing sequence of random numbers if any have been used already, earlier in the job. The NGROUPS option specifies the number of groups; the default of 10 will usually lead to recombination frequencies between the markers that form the cluster centres of about 0.1. The cluster centres are used to obtain a framework map. After ordering the markers, recombination frequencies between adjacent markers are calculated using the multi-point maximum likelihood method. The positions of the markers can be saved, in a variate, using the POSITIONS parameter. For population type CP, you can set option LINKAGEPHASES=omit to suppress determination of the linkage phases in both parents.
By default QMAP displays a genetic map, but you can set PLOT=* to suppress this. The TITLE option allows you to supply a title for the graph. Also, unless you set option PRINT=*, QMAP prints the number of linkage groups and the minimum, mean and maximum of the POSITIONS values per linkage group.
The parameters beginning with the prefix S can be used to save information sorted in ascending order according to the levels of the CHROMOSOMES factor. The SCHROMOSOMES factor contains all values of the linkage group designated '1', followed by the linkage group designated '2', and so on. The SMKNAMES parameter contains 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 are saved by the SMKSCORES parameter, and are sorted according to the SMKNAMES text. The parent information that can be saved by the SPARENTS parameter is sorted in the same way.
The OUTFILENAME option can be used to save the sorted marker scores and positions in two Flapjack files. This parameter should not contain an extension as the extension is defined automatically as .txt. The name is extended with '_geno' for the marker scores, and with '_map' for the positions.
Options: PRINT, PLOT, POPULATIONTYPE, USEPENALTY, SPATIALMETHOD, NGROUPS, MAPCHROMOSOMES, LINKAGEPHASES, TITLE, OUTFILENAME.
Parameters: MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, IDMGENOTYPES, PARENTS, IDPARENTS, SMKSCORES, SCHROMOSOMES, SPOSITIONS, SMKNAMES, SPARENTS, SEED.
Method
QMAP calculates the order of markers using simulated annealing in conjunction with spatial sampling or optimization. The spatial sampling/optimization is used to obtain a framework map; it reduces the size of the optimization problem and leads to a reduction of the effects of errors on the marker ordering. When using spatial sampling, at each step of the sampling process one marker is selected at random and all markers within a given distance, known as the sampling radius, of that marker are excluded from further sampling. Distance between markers is measured by their recombination frequencies. Sets of markers sampled in this way are more or less evenly spread along the chromosomes. The sampling radius is varied in order to order to obtain a set of markers of fixed size. When using spatial optimization, a set of framework markers is obtained by minimizing the average distance between all markers and the nearest marker in the set of framework markers, using simulated annealing. The set of markers obtained by spatial sampling is used as starting configuration for spatial optimization. Multi-point maximum likelihood estimates of recombination frequencies between adjacent markers on the genetic linkage map are obtained by the EM algorithm using a hidden Markov model.
Action with RESTRICT
Restrictions are not allowed.
References
Jansen, J., de Jong, A.G. & van Ooijen, J.W. (2001). Constructing dense genetic linkage maps. Theor. Appl. Genet., 102, 1113-1122.
Jansen, J. (2005). Construction of linkage maps in full-sib families of diploid outbreeding species by minimizing the number of recombinations in hidden inheritance vectors. Genetics, 170, 2013-2025.
Lander, E.S. & Green, P. (1987). Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA, 84, 2363-2367.
See also
Procedures: DQMAP, QLINKAGEGROUPS, QRECOMBINATIONS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
CAPTION 'QMAP example'; STYLE=meta
QIMPORT [POPULATION=F2]\
'%GENDIR%/Examples/F2maize_geno.txt';\
MKSCORES=mkscores ; MKNAMES=mknames; PARENTS=parents
QLINKAGEGROUPS [PRINT=summary; POPULATION=F2; THRESHOLD=0.30]\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
CHROMOSOMES=chromosomes
VARIATE [VALUES=1,2,7] mapchromosomes
QMAP [PRINT=summary,map ; PLOT=map,frequencies; TITLE='F2 maize';\
POPULATION=F2; SPATIAL=sampling ;\
MAPCHROMOSOMES=mapchromosomes]\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
CHROMOSOMES=chromosomes; SEED=126172
QIMPORT [POPULATION=CP]\
'%GENDIR%/Examples/CPapple_geno.txt';\
MKSCORES=mkscores ; MKNAMES=mknames; PARENTS=parents;\
IDPARENTS=idparents
QMAP [PRINT=summary,map,monitoring; PLOT=map,frequencies;\
POPULATION=CP; SPATIAL=none; TITLE='CP apple' ;\
OUTFILENAME='CPapple']\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
IDPARENTS=idparents; SPARENTS=sparents; SEED=412393