sampleIndiv: Sample Individuals from Pedigree
In optiSel: Optimum Contribution Selection and Population Genetics
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Sampling Individuals from a Pedigree.
Usage
1
sampleIndiv(Pedig, from="Born", each=100)
Arguments
Pedig
Pedigree with column Indiv and the column specified in parameter from.
from
Column name. From each cohort specified in this column (e.g. year of birth), the number of individuals specified in parameter each is sampled. If a cohort contains less individuals, then all individuals are chosen.
each
Number of individuals to be sampled from each cohort.
Details
From each cohort, a specified number of individuals will be sampled. If a cohort contains less individuals, then all individuals are sampled.
This may be needed for estimating population specific parameters from a subset of a large pedigree to reduce computation time.
Value
Character vector containing the IDs of the individuals.
Author(s)
Robin Wellmann
Examples
1
2
3
4
5
6
data("PedigWithErrors")
set.seed(1)
Pedig <- prePed(PedigWithErrors)
use <- Pedig$Breed=="Hinterwaelder"
keep <- sampleIndiv(Pedig[use, ], from="Born", each=5)
keep
Example output
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
Sire Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506
The sex of the following animals was not compatible with the pedigree, so
it was modified:
Sire Dam
276000810087663 276000802940621 276000802925028
[1] "276000802420745" "276000802420386" "276000802420682" "276000802820036"
[5] "276000802420625" "276000802420285" "276000802420484" "276000802820056"
[9] "276000802420078" "276000802420142" "276000802420207" "276000802420409"
[13] "276000802420628" "276000802420360" "276000802820072" "276000802820020"
[17] "276000802820113" "276000802420123" "276000802420233" "276000802420346"
[21] "276000802420055" "276000802420529" "276000802820043" "276000802420626"
[25] "276000802420593" "276000802420277" "276000802420511" "276000802420043"
[29] "276000802420501" "276000802420361" "276000802820168" "276000800000675"
[33] "276000802060632" "276000802420504" "276000802420079" "276000802420110"
[37] "276000802420200" "276000803611122" "276000803611123" "276000802420270"
[41] "276000802420082" "276000803611127" "276000802420538" "276000802420756"
[45] "276000802820076" "276000803611129" "276000802420025" "276000802420269"
[49] "276000802820064" "276000802280250" "276000802820109" "276000802420315"
[53] "276000802420579" "276000802820048" "276000802420712" "276000802420392"
[57] "276000802420172" "276000802820042" "276000803611144" "276000803611140"
[61] "276000802420143" "276000802820075" "276000802420135" "276000802820046"
[65] "276000802420139" "276000802420412" "276000802420512" "276000802420196"
[69] "276000802820172" "276000802420724" "276000802422668" "276000802422215"
[73] "276000803611186" "276000802422555" "276000802422209" "276000802422327"
[77] "276000803611222" "276000802825221" "276000802422343" "276000802422323"
[81] "276000802422726" "276000802422489" "276000802422460" "276000802422445"
[85] "276000802422463" "276000802423391" "276000802423346" "276000802423274"
[89] "276000803611245" "276000803611247" "276000802831834" "276000802423588"
[93] "276000802424106" "276000802424616" "276000802423987" "276000802425099"
[97] "276000802425208" "276000802425048" "276000803611271" "276000802425004"
[101] "276000802428829" "276000802427252" "276000803611305" "276000802425273"
[105] "276000802426123" "276000803622403" "276000802426274" "276000802426172"
[109] "276000802426235" "276000803611349" "276000802847521" "276000803611365"
[113] "276000802847421" "276000802843993" "276000802427567" "276000803622409"
[117] "276000802427330" "276000802427691" "276000802427299" "276000802853813"
[121] "276000802428243" "276000802856323" "276000802428354" "276000802428389"
[125] "276000802428297" "276000802862913" "276000802429242" "276000802428991"
[129] "276000802428937" "276000802428873" "276000802865630" "276000802865638"
[133] "276000802865658" "276000802866106" "276000802866021" "276000802875316"
[137] "276000802875181" "276000802875129" "276000802875170" "276000802875070"
[141] "276000802875526" "276000802883676" "276000802907816" "276000802875571"
[145] "276000802879841" "276000802883952" "276000802883843" "276000802918010"
[149] "276000802884040" "276000802918235" "276000802884325" "276000802884204"
[153] "276000802884216" "276000802884207" "276000802884125" "276000802908525"
[157] "276000802908564" "276000802884511" "276000802898219" "276000802898089"
[161] "276000802898273" "276000802898395" "276000802898772" "276000802898599"
[165] "276000802908319" "276000802898810" "276000802918549" "276000802898906"
[169] "276000802898752" "276000802898624" "276000802908263" "276000802908095"
[173] "276000802908156" "276000802908136" "276000802908282" "276000802908410"
[177] "276000802908646" "276000802908381" "276000802918213" "276000802918520"
[181] "276000802908744" "276000802907878" "276000802908727" "276000802903776"
[185] "276000802932078" "276000802918415" "276000802918330" "276000802918641"
[189] "276000802937298" "276000802918592" "276000802918683" "276000802918869"
[193] "276000802918688" "276000802918943" "276000802918623" "276000802932286"
[197] "276000802925411" "276000804741650" "276000802925669" "276000802925240"
[201] "276000802932139" "276000802925931" "276000802925986" "276000802932103"
[205] "276000802925993" "276000802932551" "276000802944711" "276000802932316"
[209] "276000891056011" "276000801393808" "276000891184172" "276000802938332"
[213] "276000802938371" "276000802938366" "276000802938539" "276000890844361"
[217] "276000802940421" "276000802937394" "276000802940680" "276000802940798"
[221] "276000802947725" "276000802947451" "276000802947405" "276000802947088"
[225] "276000891257521" "276000808406667" "276000890257818" "276000890409308"
[229] "276000808406666" "276000808336837" "276000890657297" "276000890728721"
[233] "276000808519301" "276000808519325" "276000808854502" "276000810087378"
[237] "276000890207032" "276000890257605" "276000810332402" "276000810332941"
[241] "276000890436722" "276000890295183" "276000810331374" "276000810331425"
[245] "276000890612505" "276000810958205" "276000890736617" "276000811157793"
[249] "276000810958699" "276000890601572" "276000811287356" "276000891127252"
[253] "276000810958300" "276000810787197" "276000810958905" "276000890871688"
[257] "276000811596233" "276000810748578" "276000890830017" "276000890778208"
[261] "276000891458441" "276000891243813" "276000891284660" "276000811903063"
[265] "276000891615941" "276000811903175" "276000812346791" "276000891307486"
[269] "276000812256003" "276000812346909" "276000891661503" "276000812496744"
[273] "276000812803316" "276000812497627" "276000891657068" "276000891942285"
[277] "276000891842498" "276000891928822" "276000891974304" "276000812749701"
[281] "276000813155672" "276000813255917" "276000813025168" "276000812750057"
[285] "276000892111363" "276000813609142" "276000892197681" "276000813256360"
[289] "276000813533611" "276000812939268" "276000813550109" "276000813677675"
[293] "276000891955445" "276000813368937" "276000891657435" "276000813838647"
[297] "276000892508945" "276000813907230" "276000813798399" "276000892547675"
[301] "276000892533335" "276000814117615" "276000892477922" "276000892658161"
[305] "276000814047526"
optiSel documentation built on Jan. 16, 2021, 5:30 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) Examples
Description
Sampling Individuals from a Pedigree.
Usage
1 | sampleIndiv(Pedig, from="Born", each=100)
|
Arguments
Pedig |
Pedigree with column |
from |
Column name. From each cohort specified in this column (e.g. year of birth), the number of individuals specified in parameter |
each |
Number of individuals to be sampled from each cohort. |
Details
From each cohort, a specified number of individuals will be sampled. If a cohort contains less individuals, then all individuals are sampled. This may be needed for estimating population specific parameters from a subset of a large pedigree to reduce computation time.
Value
Character vector containing the IDs of the individuals.
Author(s)
Robin Wellmann
Examples
1 2 3 4 5 6 | data("PedigWithErrors")
set.seed(1)
Pedig <- prePed(PedigWithErrors)
use <- Pedig$Breed=="Hinterwaelder"
keep <- sampleIndiv(Pedig[use, ], from="Born", each=5)
keep
|
Example output
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
Sire Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506
The sex of the following animals was not compatible with the pedigree, so
it was modified:
Sire Dam
276000810087663 276000802940621 276000802925028
[1] "276000802420745" "276000802420386" "276000802420682" "276000802820036"
[5] "276000802420625" "276000802420285" "276000802420484" "276000802820056"
[9] "276000802420078" "276000802420142" "276000802420207" "276000802420409"
[13] "276000802420628" "276000802420360" "276000802820072" "276000802820020"
[17] "276000802820113" "276000802420123" "276000802420233" "276000802420346"
[21] "276000802420055" "276000802420529" "276000802820043" "276000802420626"
[25] "276000802420593" "276000802420277" "276000802420511" "276000802420043"
[29] "276000802420501" "276000802420361" "276000802820168" "276000800000675"
[33] "276000802060632" "276000802420504" "276000802420079" "276000802420110"
[37] "276000802420200" "276000803611122" "276000803611123" "276000802420270"
[41] "276000802420082" "276000803611127" "276000802420538" "276000802420756"
[45] "276000802820076" "276000803611129" "276000802420025" "276000802420269"
[49] "276000802820064" "276000802280250" "276000802820109" "276000802420315"
[53] "276000802420579" "276000802820048" "276000802420712" "276000802420392"
[57] "276000802420172" "276000802820042" "276000803611144" "276000803611140"
[61] "276000802420143" "276000802820075" "276000802420135" "276000802820046"
[65] "276000802420139" "276000802420412" "276000802420512" "276000802420196"
[69] "276000802820172" "276000802420724" "276000802422668" "276000802422215"
[73] "276000803611186" "276000802422555" "276000802422209" "276000802422327"
[77] "276000803611222" "276000802825221" "276000802422343" "276000802422323"
[81] "276000802422726" "276000802422489" "276000802422460" "276000802422445"
[85] "276000802422463" "276000802423391" "276000802423346" "276000802423274"
[89] "276000803611245" "276000803611247" "276000802831834" "276000802423588"
[93] "276000802424106" "276000802424616" "276000802423987" "276000802425099"
[97] "276000802425208" "276000802425048" "276000803611271" "276000802425004"
[101] "276000802428829" "276000802427252" "276000803611305" "276000802425273"
[105] "276000802426123" "276000803622403" "276000802426274" "276000802426172"
[109] "276000802426235" "276000803611349" "276000802847521" "276000803611365"
[113] "276000802847421" "276000802843993" "276000802427567" "276000803622409"
[117] "276000802427330" "276000802427691" "276000802427299" "276000802853813"
[121] "276000802428243" "276000802856323" "276000802428354" "276000802428389"
[125] "276000802428297" "276000802862913" "276000802429242" "276000802428991"
[129] "276000802428937" "276000802428873" "276000802865630" "276000802865638"
[133] "276000802865658" "276000802866106" "276000802866021" "276000802875316"
[137] "276000802875181" "276000802875129" "276000802875170" "276000802875070"
[141] "276000802875526" "276000802883676" "276000802907816" "276000802875571"
[145] "276000802879841" "276000802883952" "276000802883843" "276000802918010"
[149] "276000802884040" "276000802918235" "276000802884325" "276000802884204"
[153] "276000802884216" "276000802884207" "276000802884125" "276000802908525"
[157] "276000802908564" "276000802884511" "276000802898219" "276000802898089"
[161] "276000802898273" "276000802898395" "276000802898772" "276000802898599"
[165] "276000802908319" "276000802898810" "276000802918549" "276000802898906"
[169] "276000802898752" "276000802898624" "276000802908263" "276000802908095"
[173] "276000802908156" "276000802908136" "276000802908282" "276000802908410"
[177] "276000802908646" "276000802908381" "276000802918213" "276000802918520"
[181] "276000802908744" "276000802907878" "276000802908727" "276000802903776"
[185] "276000802932078" "276000802918415" "276000802918330" "276000802918641"
[189] "276000802937298" "276000802918592" "276000802918683" "276000802918869"
[193] "276000802918688" "276000802918943" "276000802918623" "276000802932286"
[197] "276000802925411" "276000804741650" "276000802925669" "276000802925240"
[201] "276000802932139" "276000802925931" "276000802925986" "276000802932103"
[205] "276000802925993" "276000802932551" "276000802944711" "276000802932316"
[209] "276000891056011" "276000801393808" "276000891184172" "276000802938332"
[213] "276000802938371" "276000802938366" "276000802938539" "276000890844361"
[217] "276000802940421" "276000802937394" "276000802940680" "276000802940798"
[221] "276000802947725" "276000802947451" "276000802947405" "276000802947088"
[225] "276000891257521" "276000808406667" "276000890257818" "276000890409308"
[229] "276000808406666" "276000808336837" "276000890657297" "276000890728721"
[233] "276000808519301" "276000808519325" "276000808854502" "276000810087378"
[237] "276000890207032" "276000890257605" "276000810332402" "276000810332941"
[241] "276000890436722" "276000890295183" "276000810331374" "276000810331425"
[245] "276000890612505" "276000810958205" "276000890736617" "276000811157793"
[249] "276000810958699" "276000890601572" "276000811287356" "276000891127252"
[253] "276000810958300" "276000810787197" "276000810958905" "276000890871688"
[257] "276000811596233" "276000810748578" "276000890830017" "276000890778208"
[261] "276000891458441" "276000891243813" "276000891284660" "276000811903063"
[265] "276000891615941" "276000811903175" "276000812346791" "276000891307486"
[269] "276000812256003" "276000812346909" "276000891661503" "276000812496744"
[273] "276000812803316" "276000812497627" "276000891657068" "276000891942285"
[277] "276000891842498" "276000891928822" "276000891974304" "276000812749701"
[281] "276000813155672" "276000813255917" "276000813025168" "276000812750057"
[285] "276000892111363" "276000813609142" "276000892197681" "276000813256360"
[289] "276000813533611" "276000812939268" "276000813550109" "276000813677675"
[293] "276000891955445" "276000813368937" "276000891657435" "276000813838647"
[297] "276000892508945" "276000813907230" "276000813798399" "276000892547675"
[301] "276000892533335" "276000814117615" "276000892477922" "276000892658161"
[305] "276000814047526"
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.