LG3_comp: Dataset needed for build Outcrossing vignette. It is the result from compare function exemplified there.

Description

Dataset needed for build Outcrossing vignette. It is the result from compare function exemplified there.

Usage

data("LG3_comp")

Arguments

Format

List of 7 $ best.ord : int [1:51, 1:7] 43 43 22 22 7 7 7 7 7 7 ... $ best.ord.rf : num [1:51, 1:6] 0.13186 0.12343 0.12852 0.12034 0.00481 ... $ best.ord.phase: int [1:51, 1:6] 1 1 1 1 1 1 1 2 2 1 ... $ best.ord.like : num [1:51] -399 -399 -399 -399 -399 ... $ best.ord.LOD : num [1:51] 0 -0.0509 -0.1518 -0.2156 -0.2512 ... $ data.name :List of 11 ..$ geno : num [1:100, 1:52] 2 2 2 2 3 2 2 1 2 3 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:100] "IND1" "IND2" "IND3" "IND4" ... .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... ..$ n.ind : int 100 ..$ n.mar : int 52 ..$ segr.type : chr [1:52] "B3.7" "D2.18" "D1.13" "A.4" ... ..$ segr.type.num: num [1:52] 4 7 6 1 7 4 7 4 6 7 ... ..$ n.phe : num 3 ..$ pheno : num [1:100, 1:3] 43 12 20 18 34 14 12 53 22 13 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:3] "Pheno1" "Pheno2" "Pheno3" ..$ CHROM : chr [1:52] NA NA NA NA ... ..$ POS : num [1:52] NA NA NA NA NA NA NA NA NA NA ... ..$ input : NULL ..$ error : num [1:5200, 1:4] 5e-06 5e-06 5e-06 1e+00 1e+00 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:5200] "M1_IND1" "M2_IND1" "M3_IND1" "M4_IND1" ... .. .. ..$ : NULL ..- attr(*, "class")= chr [1:2] "onemap" "outcross" $ twopt :List of 8 ..$ data.name:List of 11 .. ..$ geno : num [1:100, 1:52] 2 2 2 2 3 2 2 1 2 3 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:100] "IND1" "IND2" "IND3" "IND4" ... .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. ..$ n.ind : int 100 .. ..$ n.mar : int 52 .. ..$ segr.type : chr [1:52] "B3.7" "D2.18" "D1.13" "A.4" ... .. ..$ segr.type.num: num [1:52] 4 7 6 1 7 4 7 4 6 7 ... .. ..$ n.phe : num 3 .. ..$ pheno : num [1:100, 1:3] 43 12 20 18 34 14 12 53 22 13 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : NULL .. .. .. ..$ : chr [1:3] "Pheno1" "Pheno2" "Pheno3" .. ..$ CHROM : chr [1:52] NA NA NA NA ... .. ..$ POS : num [1:52] NA NA NA NA NA NA NA NA NA NA ... .. ..$ input : NULL .. ..$ error : num [1:5200, 1:4] 5e-06 5e-06 5e-06 1e+00 1e+00 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:5200] "M1_IND1" "M2_IND1" "M3_IND1" "M4_IND1" ... .. .. .. ..$ : NULL .. ..- attr(*, "class")= chr [1:2] "onemap" "outcross" ..$ n.mar : int 52 ..$ LOD : num 3 ..$ max.rf : num 0.5 ..$ input : NULL ..$ CHROM : chr [1:52] NA NA NA NA ... ..$ POS : num [1:52] NA NA NA NA NA NA NA NA NA NA ... ..$ analysis :List of 4 .. ..$ CC: num [1:52, 1:52] 0 0.182 0.295 0.575 0.545 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. ..$ CR: num [1:52, 1:52] 0 0.818 0.295 0.509 0.455 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. ..$ RC: num [1:52, 1:52] 0 0.182 0.705 0.491 0.545 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. ..$ RR: num [1:52, 1:52] 0 0.818 0.705 0.425 0.455 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... .. .. .. ..$ : chr [1:52] "M1" "M2" "M3" "M4" ... ..- attr(*, "class")= chr [1:2] "rf_2pts" "outcross" - attr(*, "class")= chr "compare"

Details

Outcrossing vignette uses it to save time to build itself.