convertDMATRIX {AlphaBeta} | R Documentation |
calculate divergence times of the pedigree
convertDMATRIX(sample.info, branch.points, dmatrix, design)
sample.info |
input file containing information on generation times and pedigree lineages |
branch.points |
input file containing lineage branch points |
dmatrix |
input file containing 5mC divergence values for each sample pair |
design |
"sibling" or "direct" |
pedigree
## Get some toy data file1 <- system.file("extdata/dm/","sampleInfo.csv", package="AlphaBeta") file2<-system.file("extdata/dm/","branchPoints.csv", package="AlphaBeta") file3<-system.file("extdata/dm/","AB-dMatrix-CG-0.99.csv", package="AlphaBeta") sample.info <-read.table(file1,sep="\t", header=TRUE, stringsAsFactors = FALSE) branch.points <-read.table(file2,sep="\t", header=TRUE, stringsAsFactors = FALSE) dmatrix <-read.table(file3,sep="\t", header=TRUE, stringsAsFactors = FALSE) pedigree <- convertDMATRIX(sample.info=sample.info, branch.points=branch.points,dmatrix=dmatrix,design="sibling") head(pedigree)