FIXME: study geneSet class
Pedigree can be one source of information on genetic relationship
between relatives. Take for example the following pedigree:
paternal paternal maternal maternal
grandfather grandmother grandfather grandmother
| | | |
------------- -------------
| |
father mother
| |
-------------------------
|
subject
This information can be stored in a data.frame as
mother |
maternal grandfather |
maternal grandmother |
father |
paternal grandfather |
paternal grandmother |
There is considerable variability in terminology between as well as
within various fields of genetics. We use the following terms throughout
the help and code: individual (any individual in a pedigree), subject
(individual whose pedigree is given i.e. individuals in the first column
in upper data.frame), ascendant and descendant. Additionally, family,
sex, dtBirth and generation are used for additional data in the
pedigree. Their meaning should be clear. For these, argument col
is usually used in function calls.
family
TODO
ascendantSex
can be used to define sex of ascendant(s); for
example c("Male", "Female") or c("M", "F") or even c(1, 2) for father
and mother or c(2, 1, 1) for mother and two possible fathers or c(1, 1)
for father and maternal father etc. This data is needed only for the
structure of the class and defaults should be ok for the majority. But
you need to make sure that data defined here must be in accordance with
values in sex
column.
ascendantLevel
can be used to define generation level of
ascendant(s) in relation to a subject; for example c(1, 1) for father
and mother or c(1, 1, 1) for mother and two possible fathers or c(1, 2)
for father and maternal father etc. This data is needed only for the
structure of the class and defaults should be ok for the majority.
There is no need for as.integer
TODO in arguments
ascendantLevel
as this is done internally.
unknown TODO
Sex TODO
Date of birth TODO
generationOrder
defines in which order are
generation
values: "increasing" if values increase from
ascendants to descendants and "decreasing" if values decrease from
ascendants to descendants.
check
, sort
, extend
, and
codes
are actions on the pedigree and have their own help
pages.
Individuals can be stored as either integer, numeric or factor TODO. In
any case all id columns must have the same class and this is
automatically checked. Argument drop
can be used to drop unused
levels, if factors are used.
as.Pedigree.*
FIXME
as.*.Pedigree
FIXME
Object of Pedigree class is a data.frame with columns that can be
divided into core columns (subject, ascendant(s), sex, dtBirth and
generationTODO) and possibly other columns such as data on phenotype and
genotype and other subject attributes, for example factors and
covariates TODO.
Additionally, the following attributes are set on pedigree:
- .subjectcharacter, column name of subject identification in
pedigree
- .ascendantcharacter, column name(s) of ascendant(s)
identification in pedigree
- .familycharacter, column name of family identification in
pedigree
- .ascendantSexinteger, sex of ascendant(s)
- .ascendantLevelinteger, generation level of ascendant(s)
- .sexcharacter, column name of subject's sex
- .dtBirthcharacter, column name of subject's date of birth
- .generationcharacter, column name of subject's generation
- .generationOrdercharacter, generation value is "increasing" or
"decreasing" through generations
- .colClasscharacter, storage class for id columns: "integer",
"numeric" or "factor"
- .checkedlogical, is pedigree checked for common errors
- .sortedlogical, is pedigree sorted; by TODO
- .extendedlogical, is pedigree extended
- .codedlogical, is pedigree coded
- .unknownlist, uknown representation for individual
identification and other data in the pedigree; names of the list are
c(".id", ".family", ".sex", ".dtBirth", ".generation")