Description Usage Arguments Details Value Side Effects References See Also Examples
Calculate the polygenic and major gene models for quantitative trait linkage analysis using variance components approach.
1 2 3 4 |
formula |
a formula object, with the traits on the
left of a |
famid |
integer, numeric, or character vector specifying each individual's
family identifier. Members of the same family must have the same
|
id |
integer, numeric, or character vector specifying each individual's
identifier. Members of the same family must have a unique
|
dadid |
integer, numeric, or character vector specifying each individual's
father identifier. This father identifier must have the same
|
momid |
integer, numeric, or character vector specifying each individual's
mother identifier. This mother identifier must have the same
|
sex |
integer, numeric, or character vector specifying each individual's
sex. Acceptable forms of sex-coding are
|
data |
|
mloci.out |
a character value specifying a path to an mloci.out (or
similarly formatted) file. Specifying a non-empty mloci.out file will
allow multic to calculate sporadic models using the ibd (identity by
decent) information in the mloci.out file. Due to the general size of
mloci.out, it is often stored in .gz format.
|
share.out |
a character value specifying a path to a share.out (or
similarly formatted) file. This file contains the amount of
genetic material shared between each family member pair based on
family structure only. It also contains boolean values to indicate
whether two familiy members have a sibling-sibling, parent-parent, or
parent-offspring relationships. Due to the general size of
share.out, it is often stored in .gz format.
|
longitudinal |
logical flag: if |
subset |
a logical vector specifying which subset of the rows in
|
ascertainment |
vector specifying each individual's ascertainment (effected) status.
Acceptable forms of ascertainment are |
control |
|
... |
further arguments passed to
|
See the technical report.
an object of class "multic"
. See
multic.object
for more details.
Many temporary files are created during
multic
's execution. These
files are deleted afterwards (by default). If they are not deleted
(due to a crash or some other unexpected action), use the included
function clean() to delete them. Also,
multic
copies, gunzip's, and
removes the copies of share.out and mloci.out (if specified).
Amos, C. I. (1994). "Robust variance-components approach for assessing genetic linkage in pedigrees." American Journal of Human Genetics 54(3): 535-543.
Almasy, L. and J. Blangero (1998). "Multipoint quantitative-trait linkage analysis in general pedigrees." American Journal of Human Genetics 62(5): 1198-1211.
multic.object
,
multic.control
,
phi2share
,
solar2mloci
,
solar2multic
,
sw2mloci
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ## Not run:
# Call multic with a univariate formula with two covariates and no
# markers (no mloci.out argument).
fit.ibd.uni <- multic(k.trig ~ sex.x + agexam,
data = ped.phen.data,
famid, id, fa, mo, sex.x,
share.out = 'multicInput/share.out')
# Call multic with a bivariate formula with three covariates, no
# markers (no mloci.out argument), and calculate the family log
# likelihoods.
fit.ibd.bi <- multic(cbind(k.trig, k.chol) ~ sex.x + agexam + agexam2,
data = ped.phen.data,
famid, id, fa, mo, sex.x,
share.out = 'multicInput/share.out',
calc.fam.log.liks = TRUE)
# Call multic with a longitudinal formula with six covariates letting
# the kinship library calculate the share.out argument.
long.fit <- multic(cbind(sbpA, sbpB, sbpC) ~
sexA + ageA + bmiA + generA + ageAg + smkA +
sexB + ageB + bmiB + generB + ageBg + smkB +
sexC + ageC + bmiC + generC + ageCg + smkC,
data = long.data,
famid, id, dadid, momid, sex,
longitudinal = TRUE)
## End(Not run)
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