extend: Extend pedigree
In GeneticsPed: Pedigree and genetic relationship functions
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
extend finds ascendants, which do not appear as
individuals in pedigree and assigns them as individuals with unknown
ascendants in extended pedigree.
Usage
1
Arguments
x
pedigree object
ascendant
character, column names of ascendant(s), see details
col
character, column name(s) of attribute(s), see details
top
logical, add ascendants as individuals on the top or
bottom of the pedigree
Details
Argument ascendant can be used to define, which ascendants will
be extended. If ascendant=NULL, which is the default, all
ascendant columns in the pedigree are used. The same approach is used
with other pedigree attributes such as sex, generation, etc. with
argument col. Use col=NA, if none of the pedigree
attributes should be extended.
Sex of “new” individuals is infered from attribute
ascendantSex as used in Pedigree function. Generation of
“new” individuals is infered as minimal
(generationOrder="increasing") or maximal
(generationOrder="decreasing") generation value in descendants -
1. See Pedigree on this issue. Family values are extended
with means of family.
Value
Extended pedigree, where all ascendants also appear as individuals with
unknown ascendants and infered other attributes such as sex, generation,
etc. if this attributes are in the pedigree.
Author(s)
Gregor Gorjanc
See Also
Pedigree, family,
geneticGroups???
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
# --- Toy example ---
ped <- generatePedigree(nId=5, nGeneration=4, nFather=1, nMother=2)
ped <- ped[10:20,]
ped[5, "father"] <- NA # to test robustnes of extend on NA
extend(ped)
extend(ped, top=FALSE)
## Extend only ascendant and their generation
extend(ped, col="generation")
extend(ped, col=c("generation", "sex"))
# --- Bigger example ---
ped <- generatePedigree(nId=1000, nGeneration=10, nFather=100,
nMother=500)
nrow(ped)
# Now keep some random individuals
ped <- ped[unique(sort(round(runif(n=nrow(ped)/2, min=1,
max=nrow(ped))))), ]
nrow(ped)
nrow(extend(ped))
Example output
Loading required package: MASS
Attaching package: 'GeneticsPed'
The following object is masked from 'package:stats':
family
id father mother generation sex
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
110 1 NA NA 1 1
21 6 NA NA 2 1
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
id father mother generation sex
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
110 1 NA NA 1 1
21 6 NA NA 2 1
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
id father mother generation sex
1 4 NA NA 1 NA
2 9 NA NA 2 NA
3 8 NA NA 2 NA
110 1 NA NA 1 NA
21 6 NA NA 2 NA
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
id father mother generation sex
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
110 1 NA NA 1 1
21 6 NA NA 2 1
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
[1] 10000
[1] 3917
[1] 5959
GeneticsPed documentation built on Nov. 8, 2020, 5:54 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) See Also Examples
Description
extend finds ascendants, which do not appear as
individuals in pedigree and assigns them as individuals with unknown
ascendants in extended pedigree.
Usage
1 |
Arguments
x |
pedigree object |
ascendant |
character, column names of ascendant(s), see details |
col |
character, column name(s) of attribute(s), see details |
top |
logical, add ascendants as individuals on the top or bottom of the pedigree |
Details
Argument ascendant can be used to define, which ascendants will
be extended. If ascendant=NULL, which is the default, all
ascendant columns in the pedigree are used. The same approach is used
with other pedigree attributes such as sex, generation, etc. with
argument col. Use col=NA, if none of the pedigree
attributes should be extended.
Sex of “new” individuals is infered from attribute
ascendantSex as used in Pedigree function. Generation of
“new” individuals is infered as minimal
(generationOrder="increasing") or maximal
(generationOrder="decreasing") generation value in descendants -
1. See Pedigree on this issue. Family values are extended
with means of family.
Value
Extended pedigree, where all ascendants also appear as individuals with unknown ascendants and infered other attributes such as sex, generation, etc. if this attributes are in the pedigree.
Author(s)
Gregor Gorjanc
See Also
Pedigree, family,
geneticGroups???
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | # --- Toy example ---
ped <- generatePedigree(nId=5, nGeneration=4, nFather=1, nMother=2)
ped <- ped[10:20,]
ped[5, "father"] <- NA # to test robustnes of extend on NA
extend(ped)
extend(ped, top=FALSE)
## Extend only ascendant and their generation
extend(ped, col="generation")
extend(ped, col=c("generation", "sex"))
# --- Bigger example ---
ped <- generatePedigree(nId=1000, nGeneration=10, nFather=100,
nMother=500)
nrow(ped)
# Now keep some random individuals
ped <- ped[unique(sort(round(runif(n=nrow(ped)/2, min=1,
max=nrow(ped))))), ]
nrow(ped)
nrow(extend(ped))
|
Example output
Loading required package: MASS
Attaching package: 'GeneticsPed'
The following object is masked from 'package:stats':
family
id father mother generation sex
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
110 1 NA NA 1 1
21 6 NA NA 2 1
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
id father mother generation sex
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
110 1 NA NA 1 1
21 6 NA NA 2 1
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
id father mother generation sex
1 4 NA NA 1 NA
2 9 NA NA 2 NA
3 8 NA NA 2 NA
110 1 NA NA 1 NA
21 6 NA NA 2 NA
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
id father mother generation sex
1 4 NA NA 1 2
2 9 NA NA 2 2
3 8 NA NA 2 2
110 1 NA NA 1 1
21 6 NA NA 2 1
10 10 1 4 2 1
11 11 6 9 3 1
12 12 6 8 3 1
13 13 6 9 3 2
14 14 NA 8 3 2
15 15 6 8 3 1
16 16 11 13 4 1
17 17 11 13 4 1
18 18 11 14 4 1
19 19 11 13 4 2
20 20 11 14 4 2
[1] 10000
[1] 3917
[1] 5959
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.