Usage
multic(formula, data = sys.parent(), famid, id, dadid, momid, sex, mloci.out = NULL, share.out = "kinship", longitudinal = FALSE, subset = NULL, ascertainment = NULL, control = multic.control(...), ...)
Arguments
formula
a formula object, with the traits on the
left of a ~ (tilde) operator
and the covariates, separated by +
operators, on the right. The
traits may be a single numeric vector or a matrix. Commonly, traits
are aggragated together using the cbind
command. See the Examples
section for examples.
famid
integer, numeric, or character vector specifying each individual's
family identifier. Members of the same family must have the same
famid and each family must have a unique
famid. Any missing data
will result in an error message and the termination of
multic.
id
integer, numeric, or character vector specifying each individual's
identifier. Members of the same family must have a unique
id within
the family. id does not have to be
universally unique among all
individuals. Any missing data will result in an error
message and the termination of multic.
dadid
integer, numeric, or character vector specifying each individual's
father identifier. This father identifier must have the same
famid as
the individual. Any missing data will result in an
error message and the termination of multic.
momid
integer, numeric, or character vector specifying each individual's
mother identifier. This mother identifier must have the same
famid as
the individual. Any missing data will result in an
error message and the termination of
multic.
sex
integer, numeric, or character vector specifying each individual's
sex. Acceptable forms of sex-coding are
"M", "m", or
1 for male and
"F", "f", or
2 for female. Any missing data will
result in an error message and the termination of
multic.
data
data.frame in which to interpret the
variables named in formula,
famid, id,
dadid,
momid,
sex,
subset, and
ascertainment arguments. If
data is missing, the
variables in formula should be in the
search path.
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.
multic will manage this
for the user. Whether the user specifies an mloci.out file with a .gz
suffix or not will not effect how multic
operates on the file. See
solar2mloci for more details.
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.
multic will manage this
for the user. Whether the user specifies the file wiht a .gz suffix
format or not will not effect how multic
operates on the file. See
phi2share for more details.
longitudinal
logical flag: if TRUE, then fomula will
be interpreted as a
longitudinal model. In this case, the fomula argument requires
special formatting as described. The number of traits on the
left side of the ~ (tilde) is the number
of time-points for multic to
analyze. The number of covariates on the right side of the
~ (tilde)
must be a multiple of the number of traits on the left side. That
multiple is the amount of covariates to analyze at each time-point.
All covariates for the first time point must be specified before any
of the second, all second before any third, etc. See the Examples
section for examples.
subset
a logical vector specifying which subset of the rows in
data to
use in the fit.
ascertainment
vector specifying each individual's ascertainment (effected) status.
Acceptable forms of ascertainment are T,
TRUE, or 1
for a proband (effected) and F,
FALSE, or
0 for a non-proband (non-effected
person).
control
list of iteration and algorithmic
constants. See
multic.control for their names and
default values. These can also be given directly as arguments to
multic itself, instead of through a
multic.control object. If control
is specified, the arguments specified in
... will not be used.
...
further arguments passed to
multic.control to alter
multic's default behavior.
Side Effects
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).References
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.