Description Usage Arguments Value Author(s) See Also Examples
DH segmentation using genotyping data Input data requirment: genotyping data with columns of chr; pos; >=1 lines The package DNAcopy is required.
1 2 3 4 5 | genosegDH(geno, genocols, chromosomes, chrname = "chr", posname = "pos",
output.common = "seg", data.type = "logratio", allele1.name = "A",
allele2.name = "B", missing.name = c("0"), allele1.code = -1, allele2.code = 1,
min.seg.size = 1e+05, cna.alpha = 0.01, cna.nperm = 10000, cna.p.method = "perm",
cna.eta = 0.01, cna.min.width = 5, seg.mean.cutoffs = c(-0.8, 0.8))
|
geno |
genotyping data, containing at least chr; pos; genotyping scores of lines |
genocols |
column numbers of individuals |
chromosomes |
chromosomes or contigs of interest for segmentation |
chrname |
column name/num of chromosomes or contigs |
posname |
column name/num of marker positions |
output.common |
the prefix name of output file |
data.type |
binary or logratio, default logratio |
missing.name |
code for missing data, could be a vector |
min.seg.size |
minimal size of segments, segments with smaller length will be ignored |
seg.mean.cutoffs |
a numeric vector with two values, c(smaller, larger); default=c(-0.8, 0.8); default values correspond -1 and 1 as input values of allele1.code and allele2.code,respectively. segment mean values <= smaller: allele 1 segment mean values >= larger: allele 2 |
alleleX.name |
allele labels in the output |
alleleX.code |
allele codes as values for segmentation |
cna.xxx |
are DNAcopy parameters, please refer DNAcopy mannual |
output file and variable of the genotyping segmentation result
Sanzhen Liu
https://bioconductor.org/packages/release/bioc/html/DNAcopy.html
1 | genosegDH(geno = "")
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