Calculate distance matrix based of differences in genotype calls
Usage
dist.GT(object)
Arguments
object
SnpSetIllumina object
Details
Calculates distances between samples as percentage of differences in genotype
Value
'dist.GT' returns an object of class 'dist'
Author(s)
Jan Oosting
See Also
dist, hclust
Examples
data(chr17.260)
plot(hclust(dist.GT(chr17.260)))
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(beadarraySNP)
Loading required package: Biobase
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 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarraySNP/dist.GT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dist.GT
> ### Title: dist.GT
> ### Aliases: dist.GT
> ### Keywords: manip
>
> ### ** Examples
>
> data(chr17.260)
> plot(hclust(dist.GT(chr17.260)))
>
>
>
>
>
> dev.off()
null device
1
>