Calculates descriptive statistics of molecular markers (M.P. Boer & J.T.N.M. Thissen).
Options
PRINT = string tokens |
What to print (chromosomes, genome); default chro |
|---|---|
DISTANCE = scalar |
Distance between chromosomes (for plotting purposes); default 10 |
Parameters
CHROMOSOMES = factors |
Chromosome for each locus; must be set |
|---|---|
POSITIONS = variates |
Position on the chromosome for each locus; must be set |
IDLOCI = texts |
Labels for the loci |
CUMPOSITIONS = variates |
Saves the cumulative positions of the loci along the genome |
NLOCI = variates |
Saves the number of loci on each chromosome |
FIRST = variates |
Saves the index number of the first locus of each chromosome |
LAST = variates |
Saves the index number of the last locus of each chromosome |
LENGTHS = variates |
Saves the lengths of the chromosomes |
MIDDLEPOSITIONS = variates |
Saves the middle positions of the chromosomes (as cumulative positions) |
SEPARATION = variates |
Saves the positions of the gaps between chromosomes (as cumulative positions) |
GENOMELENGTH = scalars |
Saves the length of the genome |
TOTLENGTH = scalars |
Saves the total length of the genome, including added gaps between chomosomes |
Description
QDESCRIBE is mainly used as an auxiliary procedure for plotting the QTL scan profiles, calculated by the QSQTLSCAN and QMQTLSCAN procedures, and plotted by the DQSQTLSCAN and DQMQTLSCAN procedures. QDESCRIBE calculates statistics of the genome and chromosomes on the basis of chromosome identifier and locus position. The chromosome identifiers of the loci are specified by the CHROMOSOMES parameter, and the positions of the loci on the chromosomes are specified by the POSITIONS parameter. If the loci have names, these can be specified by the IDLOCI parameter. The calculated statistics can be saved using the parameters CUMPOSITIONS, NLOCI, FIRST, LAST, LENGTHS, MIDDLEPOSITIONS, SEPARATION, GENOMELENGTH and TOTLENGTH.
Options: PRINT, DISTANCE.
Parameters: CHROMOSOMES, POSITIONS, IDLOCI, CUMPOSITIONS, NLOCI, FIRST, LAST, LENGTHS, MIDDLEPOSITIONS, SEPARATION, GENOMELENGTH, TOTLENGTH.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedures: DQMQTLSCAN, DQSQTLSCAN, QMQTLSCAN, QSQTLSCAN.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
CAPTION 'QDESCRIBE example'; STYLE=meta
SPLOAD '%GENDIR%/Examples/F2maizemarkers.gwb'; SHEETNAME='LOCI'
QDESCRIBE [PRINT=chromosome,genome] CHROMOSOMES=mkchr; POSITIONS=mkpos;\
IDLOCI=idlocus; FIRST=first; LAST=last; NLOCI=nloci;\
LENGTHS=lengths; CUMPOSITIONS=cumpositions;\
MIDDLEPOSITIONS=middlepositions; SEPARATION=separation;\
GENOMELENGTH=genomelength; TOTLENGTH=totlength