R: A dummy phenotype dataset that provides an example of the...
pheno
R Documentation
A dummy phenotype dataset that provides an example of the input phenotype data used by the package
Description
A dummy dataset of 5 phenotypes measured in 150 individuals. The data has been generated to yield significant results for SNP1 and SNP2 of the snps dataset. The first two columns have been generated as alpha + beta1*snp + beta2*snp2 + error (with different alphas, betas and errors for each phenotype), the third has been generated as alpha + beta1*testPheno2 + beta2*snp3 + error, the fourth column is the results of sample of a binomial distributioni correlated with testPheno3, and the final column is the 1st PC of the principal component analysis of the snps matrix.
Format
A matrix with 150 phenotype observations.
testPheno1
a numeric vector
testPheno2
a numeric vector
testPheno3
a numeric vector
testPheno4
a numeric vector
testPheno5
a numeric vector
Details
Please note the following IMPORTANT issue: the 'pheno' matrix has both column names and row names! the column names MUST be the names of the phenotypes and the row names MUST be the codes representing each individual in the pheno matrix, one individual for each row. Both row names and column names are extracted by the main function and are therefore mandatory
Examples
data(pheno)
head(pheno)
dimnames(pheno)[[1]] # the row names
dimnames(pheno)[[2]] # the column names
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MultiPhen)
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 4.4-1).
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MultiPhen/pheno.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pheno
> ### Title: A dummy phenotype dataset that provides an example of the input
> ### phenotype data used by the package
> ### Aliases: pheno
> ### Keywords: datasets
>
> ### ** Examples
>
> data(pheno)
> head(pheno)
testPheno1 testPheno2 testPheno3 testPheno4 testPheno5
1 1.0484046 1.0882803 15.62208 1 -0.10121136
2 1.2719016 1.2676863 15.57628 1 -0.08207044
3 1.1988447 0.9678524 15.53613 1 -0.10994645
4 1.0539237 1.0119838 17.08508 0 -0.08207044
5 0.9997884 1.0417699 16.49965 0 -0.06292951
6 1.0923093 1.0879464 14.89827 1 -0.05934077
> dimnames(pheno)[[1]] # the row names
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12"
[13] "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24"
[25] "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36"
[37] "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48"
[49] "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60"
[61] "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72"
[73] "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84"
[85] "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96"
[97] "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" "108"
[109] "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" "120"
[121] "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131" "132"
[133] "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143" "144"
[145] "145" "146" "147" "148" "149" "150"
> dimnames(pheno)[[2]] # the column names
[1] "testPheno1" "testPheno2" "testPheno3" "testPheno4" "testPheno5"
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> dev.off()
null device
1
>