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This page describes how to run the C version of HAPPY. For the R version see the PDF documention.

Command-line options

HAPPY takes a number of command-line options, which can be shown by typing happy -help:

NB: Happy works on marker interval, which are always referred to by the name of the marker at the left-end of the interval.

argument	type	default value	function
-alleles	Readable File	[ ]	Name of alleles input file (see above)
-data	Readable File	[ ]	Name of data input file(see above)
-extremes	float	[ 0 ]	Only use +- extreme% phenotypes (default uses all data)
-seed	integer	[ 0 ]	Random number seed (defaults to system time
-normalize	switch	[ false ]	Transform phenotypes to be normally distributed before analysis
-pointwise	switch	[ false ]	Perfrom pointwise QTL tests rather than interval-wide (much slower)
-generations	integer	[ 60 ]	The number of generations since the HS was founded. We recommend setting this to a high value such as 500 or 1000 for maximum sensitivity, as this copes better with errors due to incorrect genotypes and wrong marker distances.
-partial	text	[ ]	Remove effect of QTL at interval with corresponding left-end marker before testing for qtls in other intervals. Used for examining multiple QTLs
-scramble	switch	[ false ]	Shuffle the phenotypes before doing any analysis
-permutations	integer	[ 0 ]	Do a permutation test at each marker location by shuffling the phenotypes this number of times and repeating the analysis of variance. Useful for checking that significant results are not artefacts caused by non-normality of the phenotypes. Warning: Slow.
-bootstrap	integer	[ 0 ]	Perform this number of bootstraps, resampling the data with replacement and repeating the analysis. Used to get confidence intervals for QTL locations. You can restrict the marker range using -bootstart, -bootstop. Warning: Very Slow.
-bootstart	text	[ ]	Specify marker at left end of first interval to be bootstrapped
-bootstop	text	[ ]	Specify marker at left end of last interval to be bootstrapped
-verbose	integer	[ 1 ]	Control level of output
-help	switch	[ ]	This help