make_seq_mappoly | R Documentation |
Makes a sequence of markers based on an object of another class.
make_seq_mappoly(input.obj, arg = NULL, data.name = NULL, genomic.info = NULL) ## S3 method for class 'mappoly.sequence' print(x, ...) ## S3 method for class 'mappoly.sequence' plot(x, ...)
input.obj |
an object of one of the following classes:
|
arg |
can be one of the following objects: i) a string 'all',
resulting in a sequence with all markers in the raw data; ii) a
string or a vector of strings |
data.name |
name of the object of class |
genomic.info |
optional argument applied for |
x |
an object of the class |
... |
currently ignored |
An object of class mappoly.sequence
, which is a
list containing the following components:
seq.num |
a |
seq.phases |
a |
seq.rf |
a |
loglike |
log-likelihood of the corresponding linkage map |
data.name |
name of the object of class
|
twopt |
name of the object of class |
Marcelo Mollinari, mmollin@ncsu.edu, with modifications by Gabriel Gesteira, gdesiqu@ncsu.edu
Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378
all.mrk <- make_seq_mappoly(hexafake, 'all') seq1.mrk <- make_seq_mappoly(hexafake, 'seq1') plot(seq1.mrk) some.mrk.pos <- c(1,4,28,32,45) (some.mrk.1 <- make_seq_mappoly(hexafake, some.mrk.pos)) plot(some.mrk.1)
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