pheno: A dummy phenotype dataset that provides an example of the...

In MultiPhen: A Package to Test for Multi-Trait Association

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

Example output

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 4.8-4).
Type 'help(meta)' for a brief overview.
  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
  [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"
[1] "testPheno1" "testPheno2" "testPheno3" "testPheno4" "testPheno5"

MultiPhen documentation built on Feb. 9, 2020, 5:07 p.m.