The genotype.saap.msa data is a multiple sequence alignment in Biostrings
AAMultipleAlignment format. It contains 120 protein sequences, each with 154
sites (SAAPs). The data is used in combination with the phenotype.aa data to
quantify the association between each amino acid substitution pair and the
phenotype vector.
Usage
data("genotype.saap.msa")
Format
AAMultipleAlignment object with 120 sequences each made of 154 amino acid
sites (SNPs), some of which qualify as single amino acid polymorphisms.
Value
AAMultipleAlignment object with 120 sequences each made of 154 amino acid
sites (SNPs), some of which qualify as single amino acid polymorphisms.
Source
http://www.ncbi.nlm.nih.gov/genbank/
Examples
data("genotype.saap.msa")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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.saap.msa.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genotype.saap.msa
> ### Title: SAAP genotype dataset (msa)
> ### Aliases: genotype.saap.msa
>
> ### ** Examples
>
> data("genotype.saap.msa")
>
>
>
>
>
> dev.off()
null device
1
>