SAAP genotype dataset

Description

The genotype.saap data is a character matrix with dimensions 120x154. It contains 154 amino acid protein sites across 120 organisms. 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)

Format

A matrix with 120 observations and 154 columns (some of which qualify as single amino acid polymorphisms).

Value

Matrix with 120 rows and 154 columns, whereby each row is a protein sequence and the elements represent an amino acids.

Source

http://www.ncbi.nlm.nih.gov/genbank/

Examples

data(genotype.saap)

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
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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.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genotype.saap
> ### Title: SAAP genotype dataset
> ### Aliases: genotype.saap
> 
> ### ** Examples
> 
> data(genotype.saap)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>