Description Usage Arguments Value Author(s) See Also Examples
Reads a synchronized file generated e.g. by the Popoolation2 software and extracts biallelic count data. Allele frequencies are polarized either by the minor or the rising allele.
1 | read.sync(file, gen, repl, polarization = c("minor", "rising", "reference"), keepOnlyBiallelic = FALSE)
|
file |
the name of the file, which the data is to be read from. |
gen |
numeric vector specifying the number of generations for each population, see 'Details'. |
repl |
numeric vector defining how populations should be grouped by replicate, see 'Details'. |
polarization |
character determining, how allele frequencies should be polarized. If |
keepOnlyBiallelic |
specifies if only polymorphic sites should be kept. Combining allele counts of all populations, monomorphic sites will always be removed. If |
read.sync
returns an object of class sync
. Allelic information, allele frequencies and sequence coverages can be accessed with various functions including af.traj
, af
and coverage
Thomas Taus
alleles
, polarization
, af.traj
, af
and coverage
1 | #MISSING
|
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