Description Usage Arguments Details Value Examples
Create an object of class ped
, from a data.frame
, required input for reassign_gen
, censor_ped
, and trim_ped
functions.
1 | new.ped(ped_file)
|
ped_file |
Data.frame. A pedigree, see details. |
The data frame supplied to new.ped
, ped_file
, must contain the following variables:
name | type | description |
FamID | numeric | family identification number |
ID | numeric | individual identification number |
dadID | numeric | identification number of father |
momID | numeric | identification number of mother |
sex | numeric | gender identification; if male sex = 0 , if female sex = 1 |
affected | logical | disease-affection status: |
affected = TRUE if affected by disease, and FALSE otherwise, |
||
Optionally, ped_file
may contain any of the following variables:
name | type | description |
available | logical | availibility status; |
available = TRUE if available, and FALSE otherwise. |
||
DA1 | numeric | paternally inherited allele at the assumed disease locus: |
DA1 = 1 if rare variant is present, and 0 otherwise |
||
DA2 | numeric | maternally inherited allele at the assumed disease locus: |
DA2 = 1 if rare variant is present, and 0 otherwise |
||
birthYr | numeric | the individual's birth year |
onsetYr | numeric | the individual's year of disease onset, when applicable, otherwise NA |
deathYr | numeric | the individual's year of death, when applicable, otherwise NA |
RR | numeric | the individual's relative-risk of disease |
Gen | numeric | the individual's generation number relative to the eldest founder. |
For the eldest founder Gen = 1, for his or her offspring Gen = 2, etc. |
||
proband | logical | proband identifier: |
proband = TRUE if individual is the proband, and FALSE otherwise. |
||
subtype | character | the individual's disease subtype, when applicable, otherwise NA |
We note that some of the optional fields above may be required for various ped functions
An object of class ped.
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