Genotypes and phenotypes of 1329 mice and 19877 SNPs from (Nicod et al. Nature Genetics 2016) for platelet counts on mouse chromosome 11Data are formatted as a binary RData list object.After downloading the data can be read into R using the command> load("chr11.PLT.Rdata")which will load a list object called "D" with the following structure:> str(D)
List of 6
$ y : num [1:1329, 1] 0.7878 2.2329 -0.3572 -0.6059 -0.0768 ...
..- attr(, "dimnames")=List of 2
.. ..$ : chr [1:1329] "Q_CFW-SW/100.0a" "Q_CFW-SW/100.0c" "Q_CFW-SW/100.0d" "Q_CFW-SW/100.0e" ...
.. ..$ : NULL
..- attr(, "scaled:center")= num 4.08
..- attr(, "scaled:scale")= num 253
..- attr(, "names")= chr [1:1329] "Q_CFW-SW/100.0a" "Q_CFW-SW/100.0c" "Q_CFW-SW/100.0d" "Q_CFW-SW/100.0e" ...
$ geno : num [1:1329, 1:19877] 0.404 0.365 0.338 -0.614 0.345 ...
..- attr(, "dimnames")=List of 2
.. ..$ : chr [1:1329] "Q_CFW-SW/100.0a" "Q_CFW-SW/100.0c" "Q_CFW-SW/100.0d" "Q_CFW-SW/100.0e" ...
.. ..$ : NULL
$ cov : num [1:1329, 1] 0 0 0 0 0 0 0 0 0 0 ...
..- attr(, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr "intercept"
$ map :'data.frame':19877 obs. of 4 variables:
..$ CHR: Factor w/ 1 level "chr11": 1 1 1 1 1 1 1 1 1 1 ...
..$ POS: int [1:19877] 3200246 3205355 3218908 3414044 3460427 3462290 3462323 3462325 3462348 3464016 ...
..$ REF: Factor w/ 4 levels "A","C","G","T": 3 4 1 1 2 1 1 4 4 1 ...
..$ ALT: Factor w/ 4 levels "A","C","G","T": 1 2 2 3 4 4 4 1 2 4 ...
$ maf : num [1:19877] 0.0511 0.0476 0.0579 0.0428 0.0389 ...
$ kinship: num [1:1329, 1:1329] 0.9969 -0.0567 -0.0784 0.855 0.0051 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:1329] "Q_CFW-SW/100.0a" "Q_CFW-SW/100.0c" "Q_CFW-SW/100.0d" "Q_CFW-SW/100.0e" ...
.. ..$ : chr [1:1329] "Q_CFW-SW/100.0a" "Q_CFW-SW/100.0c" "Q_CFW-SW/100.0d" "Q_CFW-SW/100.0e" ...
