The genotype.snp.msa data is a multiple sequence alignment in Biostrings
DNAMultipleAlignment format. It contains 51 DNA sequences, each with 100
sites (SNPs), 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.msa")
Format
DNAMultipleAlignment object with 51 sequences each made of 100 nucleotides
(SNPs).
Value
DNAMultipleAlignment object with 51 sequences each made of 100 nucleotides
(SNPs).
Source
http://mouse.cs.ucla.edu/mousehapmap/emma.html
Examples
data("genotype.snp.msa")
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.msa.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genotype.snp.msa
> ### Title: SNP genotype dataset (msa)
> ### Aliases: genotype.snp.msa
>
> ### ** Examples
>
> data("genotype.snp.msa")
>
>
>
>
>
> dev.off()
null device
1
>