dichotomous.phenotype.saap: Dichotomous phenotype dataset

Description Usage Format Value Examples


The phenotype data is a numerical vector of length 120. It represents 120 dichotomous measured phenotypes for 120 organisms. We used it as a dependent variable in combination with the genotype.saap data, and quantified the association between each of the SAAP and the phenotype.




A numerical vector with 120 elements (organisms) which correspond to the rows of he genotype data.


Vector of 120 metric elements, representing phenotypes measured for 120 organisms.



Example output

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':


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':


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, cbind, colMeans, colSums, 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, 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':


Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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


Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs
Warning message:
In data(dichotomous.phenotype.saap) :
  data set 'dichotomous.phenotype.saap' not found

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