fpederr: Simulates a pedigree with errors and missing data from a...
In pedantics: Functions to Facilitate Power and Sensitivity Analyses for Genetic Studies of Natural Populations
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Implements the 'forward' approach to producing pairs of pedigrees for power and sensitivity analyses.
Usage
1
2
3
4
Arguments
truePedigree
A complete pedigree with records for all individuals and parental ID's for all non-founders
founders
A vector the same length as the pedigree containing indicator variables 1 = founder, 0 = non-founder
sex
A vector the same length as the pedigree indicating sex, 0=male, 1=female, any other value = unknown sex
samp
A vector the same length as the pedigree indicating whether or not each individual is sampled (1), or an unsampled dummy individual (0).
sireE
Value(s) indicating the paternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
damE
Value(s) indicating the maternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
sireA
Value(s) indicating the paternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
damA
Value(s) indicating the maternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
cohort
A numeric vector the same length as the pedigree containing cohorts
first
A numeric vector the same length as the pedigree indicating the first cohort for which an individual is to be considered a potential parent
last
A numeric vector the same length as the pedigree indicating the last cohort for which an individual is to be considered a potential parent
monoecey
An indicator specifying whether or not bisexuality is allowed (0=no (default), 1=yes)
modifyAssumedPedigree
An indicator variable specifying whether or not an assumed pedigree with errors but no missing links should be supplied.
Value
assumedPedigree
A pedigree differing from the supplied pedigree
so as to mimic patterns of pedigree errors and missing data that
might occur in a real study.
truePedigree
Echos the pedigree supplied.
supplementalPedigree
(optional) a 'assumed' pedigree containing
errorsbut no missing links.
Author(s)
Michael Morrissey michael.morrissey@ed.ac.uk
References
Morrissey et al. 2007. Journal of Evolutionary Biology 20:2309-2321., Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.
See Also
Examples
1
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3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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35
36
37
testData<-as.data.frame(matrix(c(
1, NA, NA, 1, 1, 1, 2, 2,
2, NA, NA, 1, 1, 1, 2, 2,
3, NA, NA, 1, 1, 1, 2, 2,
4, NA, NA, 1, 0, 1, 2, 2,
5, NA, NA, 1, 0, 1, 2, 2,
6, 1, 4, 0, -1, 2, 3, 3,
7, 1, 4, 0, -1, 2, 3, 3,
8, 1, 4, 0, -1, 2, 3, 3,
9, 1, 4, 0, -1, 2, 3, 3,
10, 2, 5, 0, -1, 2, 3, 3,
11, 2, 5, 0, -1, 2, 3, 3,
12, 2, 5, 0, -1, 2, 3, 3,
13, 2, 5, 0, -1, 2, 3, 3,
14, 3, 5, 0, -1, 2, 3, 3,
15, 3, 5, 0, -1, 2, 3, 3,
16, 3, 5, 0, -1, 2, 3, 3,
17, 3, 5, 0, -1, 2, 3, 3),
17,8,byrow=TRUE))
names(testData)<-c("id","dam","sire","founder","sex",
"cohort","first","last")
pedigree<-as.data.frame(cbind(testData$id,testData$dam,
testData$sire))
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])
names(pedigree)<-c("id","dam","sire")
pedigree
## some missing sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
sex=testData$sex,sireA=0.5,cohort=testData$cohort,
first=testData$first,last=testData$last)$assumedPedigree
## some erroneous sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
sex=testData$sex,sireE=0.5,cohort=testData$cohort,
first=testData$first,last=testData$last)$assumedPedigree
Example output
Loading required package: MasterBayes
Loading required package: coda
Loading required package: genetics
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: MCMCglmm
Loading required package: ape
Loading required package: grid
id dam sire
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 1 4
7 7 1 4
8 8 1 4
9 9 1 4
10 10 2 5
11 11 2 5
12 12 2 5
13 13 2 5
14 14 3 5
15 15 3 5
16 16 3 5
17 17 3 5
Sorting real parents...Done.
Assigning parents for assumed pedigree...Done.
id sire dam
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 4 1
7 7 4 1
8 8 4 1
9 9 <NA> 1
10 10 5 2
11 11 <NA> 2
12 12 <NA> 2
13 13 <NA> 2
14 14 5 3
15 15 <NA> 3
16 16 <NA> 3
17 17 5 3
Sorting real parents...Done.
Assigning parents for assumed pedigree...Done.
id sire dam
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 4 1
7 7 5 1
8 8 4 1
9 9 5 1
10 10 5 2
11 11 5 2
12 12 5 2
13 13 5 2
14 14 4 3
15 15 5 3
16 16 5 3
17 17 5 3
pedantics documentation built on May 1, 2019, 10:54 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Implements the 'forward' approach to producing pairs of pedigrees for power and sensitivity analyses.
Usage
1 2 3 4 |
Arguments
truePedigree |
A complete pedigree with records for all individuals and parental ID's for all non-founders |
founders |
A vector the same length as the pedigree containing indicator variables 1 = founder, 0 = non-founder |
sex |
A vector the same length as the pedigree indicating sex, 0=male, 1=female, any other value = unknown sex |
samp |
A vector the same length as the pedigree indicating whether or not each individual is sampled (1), or an unsampled dummy individual (0). |
sireE |
Value(s) indicating the paternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
damE |
Value(s) indicating the maternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
sireA |
Value(s) indicating the paternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
damA |
Value(s) indicating the maternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
cohort |
A numeric vector the same length as the pedigree containing cohorts |
first |
A numeric vector the same length as the pedigree indicating the first cohort for which an individual is to be considered a potential parent |
last |
A numeric vector the same length as the pedigree indicating the last cohort for which an individual is to be considered a potential parent |
monoecey |
An indicator specifying whether or not bisexuality is allowed (0=no (default), 1=yes) |
modifyAssumedPedigree |
An indicator variable specifying whether or not an assumed pedigree with errors but no missing links should be supplied. |
Value
assumedPedigree |
A pedigree differing from the supplied pedigree so as to mimic patterns of pedigree errors and missing data that might occur in a real study. |
truePedigree |
Echos the pedigree supplied. |
supplementalPedigree |
(optional) a 'assumed' pedigree containing errorsbut no missing links. |
Author(s)
Michael Morrissey michael.morrissey@ed.ac.uk
References
Morrissey et al. 2007. Journal of Evolutionary Biology 20:2309-2321., Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | testData<-as.data.frame(matrix(c(
1, NA, NA, 1, 1, 1, 2, 2,
2, NA, NA, 1, 1, 1, 2, 2,
3, NA, NA, 1, 1, 1, 2, 2,
4, NA, NA, 1, 0, 1, 2, 2,
5, NA, NA, 1, 0, 1, 2, 2,
6, 1, 4, 0, -1, 2, 3, 3,
7, 1, 4, 0, -1, 2, 3, 3,
8, 1, 4, 0, -1, 2, 3, 3,
9, 1, 4, 0, -1, 2, 3, 3,
10, 2, 5, 0, -1, 2, 3, 3,
11, 2, 5, 0, -1, 2, 3, 3,
12, 2, 5, 0, -1, 2, 3, 3,
13, 2, 5, 0, -1, 2, 3, 3,
14, 3, 5, 0, -1, 2, 3, 3,
15, 3, 5, 0, -1, 2, 3, 3,
16, 3, 5, 0, -1, 2, 3, 3,
17, 3, 5, 0, -1, 2, 3, 3),
17,8,byrow=TRUE))
names(testData)<-c("id","dam","sire","founder","sex",
"cohort","first","last")
pedigree<-as.data.frame(cbind(testData$id,testData$dam,
testData$sire))
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])
names(pedigree)<-c("id","dam","sire")
pedigree
## some missing sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
sex=testData$sex,sireA=0.5,cohort=testData$cohort,
first=testData$first,last=testData$last)$assumedPedigree
## some erroneous sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
sex=testData$sex,sireE=0.5,cohort=testData$cohort,
first=testData$first,last=testData$last)$assumedPedigree
|
Example output
Loading required package: MasterBayes
Loading required package: coda
Loading required package: genetics
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: MCMCglmm
Loading required package: ape
Loading required package: grid
id dam sire
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 1 4
7 7 1 4
8 8 1 4
9 9 1 4
10 10 2 5
11 11 2 5
12 12 2 5
13 13 2 5
14 14 3 5
15 15 3 5
16 16 3 5
17 17 3 5
Sorting real parents...Done.
Assigning parents for assumed pedigree...Done.
id sire dam
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 4 1
7 7 4 1
8 8 4 1
9 9 <NA> 1
10 10 5 2
11 11 <NA> 2
12 12 <NA> 2
13 13 <NA> 2
14 14 5 3
15 15 <NA> 3
16 16 <NA> 3
17 17 5 3
Sorting real parents...Done.
Assigning parents for assumed pedigree...Done.
id sire dam
1 1 <NA> <NA>
2 2 <NA> <NA>
3 3 <NA> <NA>
4 4 <NA> <NA>
5 5 <NA> <NA>
6 6 4 1
7 7 5 1
8 8 4 1
9 9 5 1
10 10 5 2
11 11 5 2
12 12 5 2
13 13 5 2
14 14 4 3
15 15 5 3
16 16 5 3
17 17 5 3
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