pointer {pointer} | R Documentation |
This package implements mixed models of Morton & MacLean (1974), Lalouel and Morton (1981), Morton et al. (1983).
We assume that a continuous variable, x, results from the independent contributions of a major locus, a multifactorial transmissible component and random environment. Random mating is assumed. The major locus, either autosomal or sex-linked, has two alleles yielding three genotypes, with effects and prior probabilities given in Lalouel & Morton (1981). Mendelian transmission is assumed, but this has been extended. Let c~N(0,C), e~N(0,E), x~N(u,V), with V = G + C + E, where u and G are the mean effect and variance due to the major locus, as we assume cov(c,e)=cov(g,c)=cov(g,e)=0. When generation-specific heritabilities are assumed, we have X_A = g + c_A + e_A, X_K = g + c_K + e_K, V_A = G + C_A + E_A = V_K = G + C_K + E_K = V, where A and K subscripts designate adults and children respectively. Childhood heritability is denoted H = C_K/V while adult heritability is HZ = C_A/V with Z = C_A/C_K.
The iterable parameters of the models are:
V | = total variance of x. Set to 1 when only affection status is defined. |
u | = mean of x. Set of 0 when only affection status is defined. |
d | = dominance |
q | = gene frequency of the allele leading to affection or elevation of x. |
H | = childhood heritability, H = C_K/V. |
Z | = ratio of adulthood to childhood heritability, Z = C_A/C_K. |
x | = proportion of sporadic cases due to new mutants |
W | = additional random envrionmental effects relating quantitative trait x |
and libability to affection y, when so defined. If affection is defined | |
on x, set W = 0. | |
tau_1 | = p(AA transmits A). |
tau_2 | = p(Aa transmits A). |
tau_3 | = p(aa transmits A). |
R | = parent-offspring correlation of multifactorial transmissible components. |
The model requires specification of other parameters estimated prior to segregation analysis: (1). thresholds Z_{xi}, i=1, ..., n_z or affection rates I_i, i=1, ..., n_I when phenotype specification concerns only a quantitative trait of affection status but not both in a given set of data; otherwise, affection rates I_i, i=1,...,n_I but only one threshold Z_X for selection on a quantitative trait can be defined, and (2) ascertainment probabilities π_i, i=1, ...,n_Z
pointer(datfile="poidat",jobfile="poijob",profile="poipro", terfile="poiter",control=control.pointer())
datfile |
The data file. It contains individual records indicating family identification number, position within family, and other relevant information. Records for one or both parents need not be given. Only one pointer of each type may be specified. Data must be sorted by the GR field, and by PO within ID. |
jobfile |
The job file. The major control is
PT(ID=f1, PO=f2, AF=f3, QU=f4, LI=f5, PT=f6, PR=f7, GN=f8, GR=f9, SX=f10) (J or C)The first set of parentheses specifies input data fields. The second set determines joint (J) or conditional (C) probabilities, with the default being C, i.e., the probability of the phenotypes of children conditional on phenotypes of parents and pointers. Joint probabilities of parents and children, conditional on phenotype of the pointer, are not applicable to selection through parents of children. The input variables are in part optional:
|
profile |
The prolix file |
terfile |
The terse or summary file |
control |
see control.pointer |
At the moment, no value is returned and the outputs is read through the file.show function.
Morton NE, MacLean CJ (1974). Analysis of family resemblance: 3. complex segregation of quantitative traits. Am J Hum Genet 26: 489-503
Lalouel JM, Morton NE (1981). Complex segregation analysis using pointers. Hum Hered 31, 312-21
The original documentation is given as follows.
Pointer - autosomal version Written in FORTRAN, this version for a SUN workstation. This program is in three parts. 1. emx - a module used in splitting the data file for heterogeneity testing. 2. nucfama - process a file of family data. 3. rpointa - (exec = pointr), estimate segregation parameters. Files in this directory. source.emx source.nuc sorce.rpo - the set of source code. May be split to subroutines with the SUN FORTRAN 'fsplit' command or compiled with f77 to give three exec. files (emx, nucfama, pointr) make.emx make.nuc make.rpo - individual makefiles. After 'fsplit' copy each to a file 'Makefile' and give command 'make' for compilation & linking. pointer - a shell script to set up a 'cp' file that gives file assignments. poidat poijob - data & job files, an example poiter poipro - output from pointer from the example cppoi - an example 'cp' file. The documentation for this program is given in Morton N.E., Rao D.C & Lalouel J-M (1983). Methods in Genetic Epidemiology. Karger PO Box, CH-4009 Basel (Switzerland). ISBN 3-8055-3668-2
## Not run: # the documentation example pointer("poidat","poijob","poipro","poiter") file.show("poipro") file.show("poiter") ## End(Not run)