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Mouse Platelet Dataset

dataset
posted on 28.02.2020 by Richard Mott
Genotypes and phenotypes of 1329 mice and 19877 SNPs from (Nicod et al. Nature Genetics 2016) for platelet counts on mouse chromosome 11

Data 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" ...

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