Calculates a threshold to identify a significant QTL (M.P. Boer & J.T.N.M. Thissen).
|What to print (
||Type of population (
||Which method to use (
||Which type of test statistic to use (
||Defines the genome-wide significance level; default 0.05|
||Distance between evaluation points for
||Degrees of freedom for the Wald test; default 1|
||Chromosome for each locus; must be set|
||Position on the chromosome for each locus; must be set|
||The additive genetic predictors|
||The second (paternal) additive genetic predictors if
||The dominance genetic predictors if
||Saves the calculated threshold|
QTHRESHOLD calculates a genome wide significance threshold to use as a critical value to reject the null hypothesis of no QTL effect. The genome-wide type I error rate is defined by the option
ALPHALEVEL. The threshold is based on a modified Bonferroni correction. The
THRMETHOD option specifies the method for calculating the number of tests to used as the denominator. The default setting,
liji, uses the effective number of independent tests, as described by Li & Ji (2005). Alternatively, the setting
bonferroni assumes one independent test at every fixed distance on the genome, defined by the
DISTANCE option (default 4 centiMorgans). By default, the threshold is expressed as the P value on a -log10 scale, but you can set option
STATISTICTYPE=Wald to use the absolute Wald test statistic instead. Marker and map information must be supplied by the
POSITIONS parameters. The
DOMINANCEPREDICTORS parameter can supply dominance genetic predictors for population types
CP, and the
ADD2PREDICTORS parameter can supply the second (paternal) additive genetic predictors for population type
CP. The corresponding degrees of freedom for the Wald test must be set by the
DF parameter; this is equal to 1 in a single-environment QTL analysis, or to the number of environments in a multi-environment QTL analysis.
The calculated threshold can be saved using the
THRESHOLD parameter. By default the threshold is printed, but you can suppress this by setting option
QTHRESHOLD calculates a genome-wide significance threshold based on a modified Bonferonni correction, where the effective number of tests is used as the denominator instead of the total number of tests. By default the procedure estimates the effective number of independent tests by a singular value decomposition of the correlation matrix between all markers (see Li & Ji 2005 or Cheverud 2001). Alternatively,
QTHRESHOLD assumes that the effective number of tests along the genome can be approximated by n independent tests:
n = ceiling(L/D)
where L is the total genome length (in cM), D is the distance between evaluation points (in cM) supplied by the
DISTANCE option, and ceiling(x) gives the smallest integer not less than x. If the
DISTANCE option is unset, n is set to the length of the
Using the Bonferonni correction, the genome wide significance threshold T is approximated by Χ2df(1-α/n), where df is the number of degrees of freedom.
Restrictions are not allowed.
Cheverud, J.M. (2001). A simple correction for multiple comparisons in interval mapping genome scans. Heredity, 87, 52-58.
Li, J, & Ji, L. (2005). Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity, 95, 221-227.
Commands for: Statistical genetics and QTL estimation.
CAPTION 'QTHRESHOLD example'; STYLE=meta SPLOAD [PRINT=*] '%GENDIR%/Examples/F2maizemarkers.gwb'; SHEETNAME='LOCI' & '%GENDIR%/Examples/F2maizemarkers.gwb'; SHEETNAME='ADDPREDICTORS' QTHRESHOLD [THRMETHOD=liji; STATISTICTYPE=minlog; ALPHA=0.05]\ CHROMOSOMES=mkchr; POSITIONS=mkpos; ADDITIVEPREDICTORS=addpred QTHRESHOLD [THRMETHOD=liji; STATISTICTYPE=wald; ALPHA=0.05; DF=1]\ CHROMOSOMES=mkchr; POSITIONS=mkpos; ADDITIVEPREDICTORS=addpred QTHRESHOLD [THRMETHOD=liji; STATISTICTYPE=wald; ALPHA=0.05; DF=10]\ CHROMOSOMES=mkchr; POSITIONS=mkpos; ADDITIVEPREDICTORS=addpred QTHRESHOLD [THRMETHOD=bonferroni; STATISTICTYPE=wald; DF=1; DISTANCE=*]\ CHROMOSOMES=mkchr; POSITIONS=mkpos QTHRESHOLD [THRMETHOD=bonferroni; STATISTICTYPE=wald; DF=1; DISTANCE=50]\ CHROMOSOMES=mkchr; POSITIONS=mkpos QTHRESHOLD [THRMETHOD=bonferroni; STATISTICTYPE=minlog; DISTANCE=*]\ CHROMOSOMES=mkchr; POSITIONS=mkpos