genotype.snp.msa: SNP genotype dataset (msa)

In genphen: A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning

Description

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")

Example output

Loading required package: randomForest
randomForest 4.6-14
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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.3.0
Loaded modules: basemod,bugs

genphen documentation built on Nov. 8, 2020, 5:03 p.m.