FAData-class {FamAgg} | R Documentation

## Pedigree data information

### Description

`FAData` objects conveniently store pedigree along with trait information. This object is the central data structure from the `FamAgg` package. Basic usage pedigree analysis methods are described on this page and on the `PedigreeUtils` help page, familial aggregation analysis methods on the `PedigreeAnalysis` help page.

See the section about the `pedigree` `data.frame` below for a detailed description of the encoding of missing trait data or founder individuals in `FamAgg`.

### Usage

    ## S4 method for signature 'FAData'
    affectedIndividuals(object)

    ## S4 method for signature 'FAData'
    age(object)

    ## S4 replacement method for signature 'FAData'
    age(object) <- value

    ## S4 method for signature 'FAData'
    buildPed(object, id=NULL, family = NULL, max.generations.up=3,
                                max.generations.down=16, prune=FALSE, ...)

    ## S4 method for signature 'FAData'
    export(object, con, format="ped", ...)

    FAData(pedigree, age, trait, traitName, header=FALSE, sep="\t", id.col="id",
           family.col="family", father.col="father", mother.col="mother",
           sex.col="sex")

    ## S4 method for signature 'FAData'
    family(object, id=NULL, family=NULL,
                              return.type="data.frame")

    ## S4 method for signature 'FAData'
    kinship(id, ...)

    ## S4 method for signature 'FAData'
    pedigree(object, return.type="data.frame")

    ## S4 replacement method for signature 'FAData'
    pedigree(object) <- value

    ## S4 method for signature 'FAData'
    pedigreeSize(object)

    ## S4 method for signature 'FAData'
    phenotypedIndividuals(object)

    ## S4 method for signature 'FAData'
    plotPed(object, id=NULL, family=NULL, filename=NULL,
                               device="plot", symbol.related=NA,
                               proband.id=NULL, highlight.ids=NULL,
                               only.phenotyped=FALSE,
                               label1=age(object), label2=NULL, label3=NULL,
                               ...)

    ## S4 method for signature 'FAData'
    show(object)

    ## S4 method for signature 'FAData'
    trait(object, na.rm=FALSE)

    ## S4 replacement method for signature 'FAData'
    trait(object) <- value

### Arguments

(in alphabetic order)

`age` | For `FAData`: either a character(1) specifying the file name from which the age should be read or a named numeric vector of ages with the names corresponding to the ids of the individuals in the pedigree.
`con` | For `export`: the file name or connection to a file to which the pedigree information should be exported.
`device` | For `plotPed`: the device of file format in which the plot should be saved. See details for allowed values.
`family` | For `buildPed`: the id of the family for which the pedigree should be returned. For `family`: the id of the family for which the pedigree should be returned (full pedigree of the family). For `plotPed`: the id of the family for which the pedigree should be plotted.
`family.col` | For `FAData`: the name of the column containing the id of the families, if argument `pedigree` is a `character(1)` specifying the file name from which the pedigree should be read and `header` is `FALSE`.
`father.col` | For `FAData`: the name of the column containing the id of the father, if argument `pedigree` is a `character(1)` specifying the file name from which the pedigree should be read and `header` is `FALSE`.
`filename` | For `plotPed`: a character string specifying the name of the file to which the plot should be saved. If none is submitted, the plot is saved to a temporary file.
`format` | For `export`: the format in which the pedigree should be exported. At present only `"ped"` and `"fam"` are exported, i.e. the file formats from plink (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml).
`header` | For `FAData`: only used if argument `pedigree` is a `character(1)`, i.e. the file name from which the pedigree should be read. The `header` argument is passed to the `read.table` function, i.e. should be set to `TRUE` if the file contains column headers.
`highlight.ids` | A list of character vector(s) of ids that should be labeled. The name(s) of the character vector(s) is/are used as the text to label the individuals (the text is shown below the symbol of the individuals). Up to 3 character vectors are supported. Alternatively, a single character vector of ids can be submitted in which case the individuals are labeled with an asterisc (`"*"`).
`id` | For method `kinship`: the `FAData` object from which the kinship matrix should be extracted, for all other methods the id of the individual. For method `plotPed`: the id of the individual for which the pedigree should be built (see `buildPed`) and plotted. Note: `id` can be a `numeric` or a `character`. Numeric ids are internally converted to `character`.
`id.col` | For `FAData`: the name of the column containing the id of the individuals, if argument `pedigree` is a `character(1)` specifying the file name from which the pedigree should be read and `header` is `FALSE`.
`label1` | For `plotPed`: labels that should be plotted below the symbol for each individual. Should be either a named vector with names corresponding to the ids of the individuals in the pedigree or a vector of the same length than individuals that are to be plotted. For the former it is sufficient to just specify the labels for the individuals that should be shown.
`label2` | For `plotPed`: see `label1`. The labels are plotted in the second line below the symbol if `HaploPainter` is used to generate the plot, or on the top left corner of the individual's symbol for `kinship2` plotting.
`label3` | For `plotPed`: see `label1`. The labels are plotted in the third line below the symbol if `HaploPainter` is used to generate the plot, or on the top right corner of the individual's symbol for `kinship2` plotting.
`max.generations.down` | For `buildPed`: the maximal number of generations to look for children.
`max.generations.up` | For `buildPed`: the maximal number of generations to look for ancestors.
`mother.col` | For `FAData`: the name of the column containing the id of the mother, if argument `pedigree` is a `character(1)` specifying the file name from which the pedigree should be read and `header` is `FALSE`.
`na.rm` | For `trait`: whether missing values in trait should be returned or not.
`object` | The `FAData` object.
`only.phenotyped` | Wheter only phenotyped individuals, i.e. individuals with a non-NA value in column `affected` (the trait information). Requires this information to be present.
`pedigree` | For `FAData`: either a `data.frame` with the pedigree information or a `character(1)` specifying the file name from which the pedigree should be read. See description below for more details.
`proband.id` | For `plotPed`: character vector with the id(s) of one ore more individuals that should be highlighted as probands. `HaploPainter` indicates probands with a `"P"` next to the symbol and an arrow pointing to the symbol.
`prune` | For `buildPed`: whether the smallest possible (connected) pedigree for the submitted ids should be build. This makes only sense if more than one id is submitted.
`return.type` | Either `"data.frame"` or `"pedigree"` if the pedigree information should be returned as a `data.frame` or `pedigreeList` object as defined in the `kinship2` package.
`sep` | For `FAData`: only used if argument `pedigree` is a `character(1)`, i.e. the file name from which the pedigree should be read. The `sep` argument is passed to the `read.table` function and specifies the field separator.
`sex.col` | For `FAData`: the name of the column spefifying the sex of the individuals, if argument `pedigree` is a `character(1)` representing the file name from which the pedigree should be read and `header` is `FALSE`.
`symbol.related` | For `plotPed`: the symbol which should be used to label individuals sharing kinship with the id for which the pedigree is generated and plotted.
`trait` | For `FAData`: a numeric vector with `0`, `1` and `NA` or a logical vector indicating unaffected (but phenotyped), affected and not phenotyped individuals.
`traitName` | For `FAData`: an optional name for the trait.
`value` | For `age<-`: a named numeric vector. The names (at least some of them) have to match the ids in the pedigree of the object. For `pedigree<-`: For `trait<-`: a named numeric vector with `0`, `1` and `NA` or a logical vector with `FALSE`, `TRUE`, `NA` for not affected, affected and not tested. The names (at least some of them) have to match the ids in the pedigree of the object.
`...` | Additional arguments to be passed to the functions (`doPlotPed` for `plotPed`).

### Details

See sections below for a description of the individual methods.

The `buildPed` method is a combination of the methods `getAncestors`, `getChildren` and `getMissingMate`, i.e. it first gets all ancestors for the specified id(s), determines then the children of all of the ids (submitted ids and their ancestors) and at last looks for any missing mates/spouses to complete the pedigree.

The `plotPed` function uses either the external perl program `HaploPainter` or the plotting capabilities of the `kinship2` package. With `HaploPainter`, as it is an external too, it is not possible to display the plot directly, but each plot is automatically saved to a file (either `"pdf"`, `"ps"`, `"svg"` or `"png"`; can be specified with the `device` parameter). `HaploPainter` plotting supports also `device = "txt"` in which case the data table is exported (in the format expected by `HaploPainter`) to a tabulator delimited text file and the name of this text file is returned - no plot is created. Plotting with `kinship2` (the default) allows to display the plot (`device="plot"`) or export it to a file (`device="pdf"` or `device="png"`).

The `switchPlotfun` function can be used to change the plotting system.

### Value

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

### Objects from the Class

`FAData` objects are created by the constructor function `FAData` and should not be directly created by a call to `new`.

### Slots

age

  A (named) numerical vector with the age of the individuals. It is suggested to use the getter and setter methods described below to access this slot.

pedigree

  A `data.frame` with the pedigree. It is suggested to use the getter and setter methods described below to access this slot.

.kinship

  The kinship matrix for the kinship of each individual in the pedigree with each other. This slot should not be accessed directly, but the `kinship` method should be used instead.

traitname

  The name of the trait being stored in the object.

.trait

  A numerical vector with the trait information, `0`, `1`, `NA`, for phenotyped but not affected, affected and not tested, respectively. This slot should not be accessed directly, but the `trait` and `trait<-` methods should be used instead that ensure that the data is matched to the information in the pedigree.

### Constructors, importing and exporting data

FAData

  Constructor function to create a new `FAData` instance. In addition to submitting the pedigree information as `data.frame`, `pedigree` or `pedigreeLinst` it is possible to specify the name of the file from which the pedigree information should be read. The recognizes and imports plink ped and `fam` files (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) or from generic text files. For the latter, arguments `header`, `sep`, `family.col`, `id.col`, `father.col`, `mother.col` and `sex.col` allow to further specify which columns of the file contain what information etc. If argument `pedigree` is a `data.frame`, the column names `"family"`, `"id"`, `"father"`, `"mother"` and `"sex"` are expected. Any additional columns are dropped.

  The sex is expected to be encoded either as a numeric 1 (male), 2 (female) with any other number or `NA` representing unknown, or as a character vector or factor with `"M"`, `"m"`, `"Male"` or `"male"` for male and `"F"`, `"f"`, `"Female"` or `"female"` for female.

export

  Export pedigree data to a file.

### Accessors and subsetting

object$name

  Access `name` column in the pedigree of the `FAData` object. The function returns a named vector wirh the names corresponding to the ids of the individuals or `NULL` if `name` does not correspoind to a column name in the pedigree. The trait data can be accessed either by `object$trait` or `object$affected`.

age

  Returns the age of the individuals as a named numeric vector. If the pedigree is set, the order of the values corresponds always to the ordering of the individuals in the pedigree with `NA` for individuals for which the age is unknown. In case the age was never set it returns a vector of NAs with length equal to the number of individuals.

age<-

  Setter for the age. Value has to be a named numeric vector.

pedigree

  Returns the pedigree either as a `data.frame` or a `pedigreeList` object (defined in the `kinship2` package) depending on the value of the parameter `return.type` (i.e. either `return.type="data.frame"` or `return.type="pedigree"`). If `pedigree` is called on any other object than a `FAData` object (or any object that inherits from that object), the `pedigree` method from the `kinship2` package is called.

  For the default return type (i.e. `return.type="data.frame"`) a `data.frame` is returned with the following columns: `"family"`: the ID of the family, `"id"`: the ID of the individual, `"father"`: the ID of the individual's father. Founder individuals, i.e. individuals for whom the father and mother is not known in the data set, contain a `NA` in this column. `"mother"`: the ID of the individual's father. Founder individuals, i.e. individuals for whom the father and mother is not known in the data set, contain a `NA` in this column. `"sex"`: the sex of the individuals encoded as a `factor` with levels `"M"` and `"F"` for male and female, or `NA` for not known. If trait information is available in the object the returned `data.frame` will also contain a column named `affected` with the information whether the individual is affected (`1`), not affected (`0`) or was not tested/phenotyped `NA`.

pedigree<-

  Setter for the pedigree slow. Value can be a `data.frame` with columns containing the family id, individual id, father id, mother id and sex (in this order) or a `pedigree` or `pedigreeList` object as defined in the `kinship2` package.

object[i, ]

  Subsets the `FAData` object to individuals specified with `i` which can be a logical, numeric or character vector. For the latter, the elements have to be the ids of the individuals (i.e. rownames of `pedigree(object)`). Returns the sub-setted object. Note that subsetting other than by family might result in a non-valid pedigree (e.g. if mother or father ID are not available in the sub-setted pedigree).

trait

  Get the trait vector from the object. By default, the ordering is the same as pedigree, setting argument `na.rm=TRUE` removes all `NA` values, thus the ordering and length might be different. Returns a named vector with the names corresponding to the ids of the individuals.

trait<-

  Setter for the trait slot. Can be a named numeric vector (values `0`, `1` and `NA`) or logical vector (values `FALSE`, `TRUE` and `NA`) with the names matching the ids of the individuals in the pedigree. The method internally matches and re-orders the trait vector to match the ordering of the ids in the pedigree.

### Basic usage

affectedIndividuals

  Returns a character vector with the ids of the affected individuals, i.e. the id of the individuals with a value other than 0 or `NA` in the trait. If no trait data is available the method returns `NULL`.

buildPed

  Builds a pedigree for the specified id(s) containing generations defined by `max.generations.up` and `max.generations.down` and returns it as a `data.frame`. The pedigree contains all individuals in the family sharing kinship with the input individual(s) and mates needed to complete the pedigree. For `prune=TRUE` the function tries to find the smallest connected pedigree for all the submitted ids.

family

  Returns the pedigree for a full family. In contrast to `buildPed` which constructs a (sub)pedigree for a specific individual, this method returns the pedigree of the complete family for an individual (if `id` is specified). The function returns either a `data.frame` or a `pedigreeList` with the pedigree for the family.

kinship

  Extracts the pre-calculated kinship matrix, i.e. a symmetric matrix with the kinship between all individuals in the pedigree. The matrix is calculated using the `kinship` method provided by the `kinship2` package [Sinwell (2014)]. The function returns a `dsCMatrix` from the `Matrix` package.

pedigreeSize

  Returns the size, i.e. the number of individuals (rows) in the pedigree.

phenotypedIndividuals

  Returns a character vector with the ids of the phenotyped individuals, i.e. the id of all individuals that have a non-NA value in thetrait. If no trait data is available the method returns `NULL`.

plotPed

  Creates the pedigree for the submitted id(s) or family and plots it (i.e. saves it to the specified file). See details above for more information. Returns the file name of the file to which the pedigree plot was exported or `NULL` for `kinship2` plotting and `device="plot"`.

  For `HaploPainter` plotting and `device = "txt"` the name of the file to which the plotting data has been exported is returned.

  See `doPlotPed` for more information.

### Pedigree analysis methods

Methods for familial aggregation and other pedigree analysis methods are described on the PedigreeAnalysis help page.

### Pedigree utilities

A variety of different pedigree utilities are defined for `FAData` objects. For the full list of methods see the PedigreeUtils help page.

### Note

The ids of individuals, father, mother and family can be either numeric or characters, internally, all ids will however be handled as characters.

The `pedigree<-` setter method removes all white spaces in columns `"id"`, `"family"`, `"father"` and `"mother"` of the pedigree.

### Author(s)

Johannes Rainer.

### References

Sinwell JP, Therneau TM & Schaid DJ (2014) The kinship2 R package for pedigree data. Human heredity 78:91-93.

### See Also

`pedigree`, `FAProbResults`, `FAKinGroupResults`, `FAKinSumResults`, `FAGenIndexResults`, `doPlotPed`, `PedigreeUtils`, `getAll`, `PedigreeAnalysis`

### Examples

    ##########################
    ##
    ##  Create a new FAData object
    ##
    ## 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")
    ## Defining the optional argument age.
    Age <- mbsub$endage
    names(Age) <- mbsub$id
    ## Create the object
    fad <- FAData(pedigree=mbped, age=Age)

    fad

    ## Extract the ids directly...
    head(fad$id)

    ## Extract the kinship matrix
    dim(kinship(fad))

    ## What's the size of the pedigree?
    pedigreeSize(fad)

    ## Importing a "ped" file.
    pedFile <- system.file("txt/minnbreastsub.ped.gz", package="FamAgg")
    ## Quick glance at the file.
    readLines(pedFile, n=1)
    fad <- FAData(pedFile)

    head(pedigree(fad))

    ## Creating the FAData reading data from a txt file.
    pedFile <- system.file("txt/minnbreastsub.txt", package="FamAgg")
    fad <- FAData(pedigree=pedFile, header=TRUE, id.col="id",
                  family.col="famid", father.col="fatherid",
                  mother.col="motherid")
    ## Adding the age
    age(fad) <- Age
    fad
    ## List all families in the pedigree along with the number of
    ## individuals
    table(fad$family)

    ##########################
    ##
    ##  Basic usage
    ##
    ## Extracting the pedigree information
    ped <- pedigree(fad)
    ## By default the pedigree is returned as a data.frame.
    class(ped)
    head(ped)

    ## In addition, we can extract the pedigree as a pedigreeList
    pedigree(fad, return.type="pedigree")

    ## Return the ids of all ancestors of individual 6
    ## up to 3 generations
    getAncestors(fad, id="6")

    ## Build the pedigree for individual 6: this includes all of its
    ## children and all of its ancestors up to the maximal number of
    ## specified generations.
    buildPed(fad, id=6)
    ## Which is a sub-pedigree of the complete family:
    family(fad, id=6)

    ## In addition we can specify manually some ids in the pedigree and
    ## generate the smallest possible pedigree containing all ids:
    buildPed(fad, id=c(6, 23, 28), prune=TRUE)

    ## Get the list of all ids sharing kinship with individuals
    ## 5 and 9
    shareKinship(fad, id=c("5", "9"))

    ## Subset the fad to family "4"
    subFad <- fad[fad$family == "4", ]
    subFad

    ## Export the pedigree from this family to a ped file
    tmpFile <- tempfile()
    export(subFad, con=tmpFile, format="ped")

    head(read.table(tmpFile, sep="\t"))

    ##########################
    ##
    ##  Plotting
    ##
    ## Plot the pedigree for individual 6.
    plotPed(fad, id=6)

    ## Alternatively, exporte it to a temporary file
    pfile <- plotPed(fad, id=6, device="pdf")
    pfile

    ## Highlighting some of the individuals:
    ## first get to know which other individuals are in the pedigree
    plotPed(fad, id=6, highlight.ids=list(hello=c(1, 2, 4)))

    ##########################
    ##
    ##  Adding trait data
    ##
    fad <- FAData(pedigree=mbped, age=Age)
    tcancer <- mbsub$cancer
    names(tcancer) <- mbsub$id
    trait(fad) <- tcancer
    ## Now we can plot the pedigree also showing the affected status.
    plotPed(fad, id=6)

    ## Alternatively, create the FAData with the trait data
    fad <- FAData(pedigree=mbped, trait=mbsub$cancer, traitName="cancer")
    plotPed(fad, id=6)

[Package FamAgg version 1.6.1 Index]