defineControls: Define sets of control individuals for one or more given...
In jotsetung/FamAgg: Pedigree Analysis and Familial Aggregation

getAll

R Documentation

Define sets of control individuals for one or more given individuals

Description

These functions allow to define sets of (eventually matched) control individuals for one or more given individuals using pedigree data. By default, controls from the same family than the specified individual(s) are returned. They are used e.g. in the genealogicalIndexTest method.

Usage


## S4 method for signature 'data.frame'
getAll(object, id=NULL, ...)

## S4 method for signature 'data.frame'
getExternalMatched(object, id=NULL, match.using, ...)

## S4 method for signature 'data.frame'
getGenerationMatched(object, id=NULL,
                                           include.anc=0, include.off=0, ...)

## S4 method for signature 'data.frame'
getGenerationSexMatched(object, id=NULL,
                                               include.anc=0, include.off=0, ...)

## S4 method for signature 'data.frame'
getSexMatched(object, id=NULL, ...)

Arguments

(in alphabetic order)

`id`	A character vector with ids of individuals for whom matched control individuals (from the same family) should be defined.
`include.anc`	For `getGenerationMatched` and `getGenerationSexMatched`: number of ancestor generations of individuals `id` in which control individuals should be defined, in addition to the actual generation of the individuals `id`. By default the functions define control individuals only in the actual generation of the individuals in `id`.
`include.off`	For `getGenerationMatched` and `getGenerationSexMatched`: number of offspring generations of individuals `id` in which control individuals should be defined, in addition to the actual generation of the individuals `id`. By default the functions define control individuals only in the actual generation of the individuals in `id`.
`match.using`	For `getExternalMatched`: a named vector for matching of controls. The names of the vector have to correspond to the ids of the individuals in the pedigree (but can have a different ordering).
`object`	Either a `data.frame`, `pedigree` or a `pedigreeList` object specifying the pedigree. If a `data.frame` is submitted, the columns `id`, `family`, `father`, `mother` and `sex` are required.
`...`	Additional arguments; not used at present.

Value

Refer to the method and function description above for detailed information on the returned result object.

Get matched controls

getAll: Simply returns the ids of all individuals in the family (i.e. individuals with the same family id in the pedigree) of the specified ids in id. Returns a list with the ids (of type character) of the controls. The names of the list correspond to the family id.
getExternalMatched: Returns the ids of matched individuals from the same family for the specified ids in id. The match.using vector is for the matching, i.e. the function first extracts the values for the individuals in id from match.using and returns the ids of all individuals whose value in match.using matches the value of the individuals specified by id. Individuals with a missing value in match.using are excluded. Returns a list with the ids (of type character) of the controls. The names of the list correspond to the family id.
getGenerationMatched: Returns the ids of individuals matched by the generation of the individuals in id. The function returns the ids of all individuals from the same generation(s) than the individuals in id. The arguments include.anc and include.off can be used to increase the range of generation from which individuals are selected. Returns a list with the ids (of type character) of the controls. The names of the list correspond to the family id.
getGenerationSexMatched: Same as getGenerationMatched, but matches in addition individuals by sex (see getSexMatched). Returns a list with the ids (of type character) of the controls. The names of the list correspond to the family id.
getSexMatched: Returns ids of individuals from the same family matching the sex of the individuals in id. Individuals with sex being NA are excluded. The result is essentially identical to the getAll if id contains ids of male and female individuals. Returns a list with the ids (of type character) of the controls. The names of the list correspond to the family id.

Author(s)

Johannes Rainer.

Examples

##########################
##
##  Defining a small pedigree
##
## load the Minnesota Breast Cancer record and subset to the
## first families.
data(minnbreast)
mbsub <- minnbreast[minnbreast$famid==4 | minnbreast$famid==5, ]
mbped <- mbsub[, c("famid", "id", "fatherid", "motherid", "sex")]
## renaming column names
colnames(mbped) <- c("family", "id", "father", "mother", "sex")

## Get ids of individuals from the same generation than "4"
getGenerationMatched(mbped, id="4")

## Get the ids of gemale individuals from the same generation than
## "4" and "22"
getGenerationSexMatched(mbped, id=c("4", "22"))

## Generate a FAData
fad <- FAData(mbped)

## Plot the pedigree so we can evaluate the results of the function
plotPed(fad, family="4")

## We're using getExternalMatched on the sex of the individuals
## in the pedigree, thus the results are identical to the
## getSexMatched function.
## Extracting the sex using $sex returns a named vector just
## as we need for getExternalMatched.
head(fad$sex)
getExternalMatched(fad, id="4", match.using=fad$sex)

getSexMatched(fad, id="4")

jotsetung/FamAgg documentation built on March 15, 2023, 3:48 a.m.