Calculates the expected numbers of recombinations and the recombination frequencies between markers (J. Jansen, J.T.N.M. Thissen & M.P. Boer).
Options
PRINT = string tokens |
What to print (summary, positions); default summ |
|---|---|
PLOT = string token |
What to plot (frequencies); default freq |
TITLE = text |
General title for the plot |
POPULATIONTYPE = string token |
Type of population (F2, BC1, RIL, DH1, CP); must be set |
METHOD = string token |
Which method to use (twopoint, multipoint); default twop |
USEPENALTY = string token |
Whether to increase the number of recombinations when METHOD=twopoint by 0.5 recombination per informative meiosis for each missing marker score (yes, no); default no |
Parameters
MKSCORES = pointers |
Marker scores for each marker; must be set |
|---|---|
CHROMOSOMES = factors |
Factor defining the linkage groups |
POSITIONS = variates |
Saves the positions of the markers when METHOD=multipoint |
MKNAMES = texts |
Names of the markers; must be set |
PARENTS = pointers |
Marker scores of the parents; must be set |
ORDER = variates |
Order of the markers for METHOD=multipoint |
NRECOMBINATIONS = symmetric matrices or pointers |
Saves the number of recombinations |
RECFREQUENCIES = symmetric matrices or pointers |
Saves the recombination frequencies |
PHASESWITCHES = pointers |
Saves the phase switches for pairs of markers when POPULATIONTYPE=CP |
INHERITANCEVECTORS = pointers |
Saves the inheritance vectors when METHOD=multipoint |
GENNRECOMBINATIONS = variates |
Saves the numbers of recombinations of the genotypes when METHOD=multipoint |
Description
QRECOMBINATIONS calculates the expected numbers of recombinations, and the recombination frequencies between markers, from the marker scores. 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 PARENTS parameter. The CHROMOSOMES parameter can be set if the markers do not belong to the same linkage group. The POPULATIONTYPE option must be set to specify the type of population from which the marker scores have been obtained.
The METHOD option specifies whether the numbers of recombinations are calculated by the two-point or multi-point method. The default, METHOD=twopoint, must be used if the order of the markers is not available. The USEPENALTY option then controls whether the number of recombinations is increased by 0.5 recombination per informative meiosis for each missing marker score. For METHOD=multipoint the order of the markers must be supplied, using the ORDER parameter.
The numbers of recombinations and the recombination frequencies can be saved using the NRECOMBINATIONS and RECFREQUENCIES parameters, respectively. These usually save a symmetric matrix. However, when POPULATIONTYPE=CP, the numbers of recombinations and recombination frequencies of the maternal and paternal meiosis are estimated separately, and so they each save a pointer containing two symmetric matrices. The PHASESWITCHES parameter saves the phase switches in the maternal and paternal meiosis for pairs of markers, in pointers of symmetric matrices. The value of the phase switch is set to one if the saved recombination frequency is equal to one minus the observed recombination frequency, and zero otherwise.
When METHOD=multipoint the positions of the markers are calculated, and can be saved in a variate using the POSITIONS parameter. The inheritance vectors and expected numbers of recombinations of the genotypes can then also be saved, using the INHERITANCEVECTORS and GENNRECOMBINATIONS parameters, respectively.
The PRINT option controls the printed output. The default setting, summary, prints the minimum, mean and maximum of the NRECOMBINATIONS values. When METHOD=multipoint, the positions setting can be used to print the minimum, mean and maximum of the POSITIONS values.
The default setting, frequencies, of the PLOT option plots the frequencies in a shaded diagram. The TITLE option can be used to provide a title for the plot.
Options: PRINT, PLOT, TITLE, POPULATIONTYPE, METHOD, USEPENALTY.
Parameters: MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, PARENTS, ORDER, NRECOMBINATIONS, RECFREQUENCIES, PHASESWITCHES, INHERITANCEVECTORS, GENNRECOMBINATIONS.
Method
For the two-point method, QRECOMBINATIONS estimates the expected numbers of recombinations and maximum likelihood estimates of the recombination frequencies of pairs of markers by the EM algorithm, using the formula
rNew = E(R|marker data, rCurrent),
where R denotes the number of recombinations, and rCurrent and rNew denote the current and new values of the recombination frequency. The estimation requires iteration only when POPULATIONTYPE=F2 or in some cases when POPULATIONTYPE=CP; see Maliepaard, Jansen & van Ooijen (1997). In all other cases estimation only requires simple counting of recombinations.
For the multi-point method, QRECOMBINATIONS follows essentially the same procedure for estimating the recombination frequencies between adjacent markers in a sequence of markers, using hidden Markov models (HMM); see Lander & Green (1987).
Action with RESTRICT
Restrictions are not allowed.
References
Maliepaard, C., Jansen J. & van Ooijen J.W. (1997). Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet. Res., Camb, 70, 237-250.
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: QLINKAGEGROUPS, QMAP.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QRECOMBINATIONS examples'; STYLE=meta
QIMPORT [POPULATION=F2]\
'%GENDIR%/Examples/F2maize_geno.txt';\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents
QRECOMBINATIONS [POPULATION=F2; METHOD=twopoint; TITLE='F2 maize']\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents
QIMPORT [POPULATION=CP]\
'%GENDIR%/Examples/CPapple_geno.txt';\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents
QRECOMBINATIONS [POPULATION=CP; METHOD=twopoint; TITLE='CP apple']\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
RECFREQUENCIES=recfreq
PRINT recfreq[1]
PRINT recfreq[2]