The genotype.snp data is a character matrix with dimensions 51x100.
It contains 100 SNPs across 51 mouse strains, taken from the publicly
available Mouse Hapmap data. We used it in combination with the
phenotype.snp data to compute the association between each SNP and
the phenotype data.
Usage
data(genotype.snp)
Format
A matrix with 51 observations (laboratory mouse strains) and 100
variables (SNPs).
Value
Matrix with 51 rows and 100 columns, whereby each column is a SNP,
and the elements represent an alleles (nucleotides).
Source
http://mouse.cs.ucla.edu/mousehapmap/emma.html
Examples
data(genotype.snp)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(genphen)
Loading required package: randomForest
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.
Loading required package: e1071
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:randomForest':
margin
Loading required package: effsize
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:randomForest':
combine
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genphen/genotype.snp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genotype.snp
> ### Title: SNP genotype dataset
> ### Aliases: genotype.snp
>
> ### ** Examples
>
> data(genotype.snp)
>
>
>
>
>
> dev.off()
null device
1
>