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Mouse Platelet Dataset

dataset
posted on 28.02.2020, 14:56 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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