Summary: Analyze pedigree data Argument: < file name >
The main analysis command in GENEHUNTER is the "scan" command. For each pedigree found in the file indicated, the "scan" command will compute LOD scores and NPL sharing statistics at many positions in the genetic map (entered in the locus parameter file or via the "use" command). In addition, if the "count recs" option is turned on, observed recombinations will be displayed for each map interval at the end of the scan for each pedigree. This can be useful in highlighting likely positions of errors in the data.
The pedigree should be in the Linkage pedigree input format (before running MAKEPED or doing any preprocessing!). Each line of this file must have the following structure:
3 12 8 9 1 2 1 1 2 8 3 0 0 4 6 1 3 ...
(a) (b) (c) (d) (e) (f) (g) (h ------------------------)
(a) pedigree name
(b) individual ID #
(c) father's ID #
(d) mother's ID #
(e) sex (1=MALE, 2=FEMALE)
(f) affectation status (1=UNAFFECTED, 2=AFFECTED)
(g) liability class (OPTIONAL) -
classes specified in marker data file
(h) marker genotypes
A 0 in any of the disease phenotype or marker genotype positions
(as in the the genotypes for the third marker above) indicates
missing data. See the file linkped.pre as an example.
A - in the phenotype/covariate data indicates missing data - NB:
0 is a real value that a phenotype may take on and DOES NOT represent
missing phenotype data
In this file format, you may enter as many pedigrees as you wish in a single file. If a pedigree is too large to be computed using a reasonable amount of time and memory, some individuals that provide less information will be discarded and warnings will be printed. Unaffected individuals with no descendents in the pedigree may be discarded with minimal loss of information and these will be the first eliminated should the pedigree be too large. See the "discard" option if you wish to utilize this speed-up in general.
The scan output of each pedigree consists of up to 5 columns of information (depending on the setting of 'analysis type') as follows:
cM position in the scan
LOD score
(computed using the disease model given in the parameter file)
NPL statistic
exact computed significance (p-value)
information content of the genotype data
The "total stat" command may be run after a successful "scan" to see the total scores for the entire data set.
IMPORTANT : Keep in mind when creating files that there must be a one-to-one correspondence (IN ORDER AND NUMBER) between the markers described in the marker data file and the markers that have genoptypes listed for them in the pedigree file.