read.sync: Read Sync-File Format
In popgenvienna/poolseq: Simulate and Analyze Pool-seq Data

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 `polarization = "minor"` (default) allele counts are polarized for the minor allele. If `polarization = "rising"` or `polarization = "reference"` then allele counts are polarized for the rising or reference allele, respectively.
`keepOnlyBiallelic`	specifies if only polymorphic sites should be kept. Combining allele counts of all populations, monomorphic sites will always be removed. If `keepOnlyBiallelic = FALSE` (default), then also triallelic sites will be kept. Otherwise (`keepOnlyBiallelic = TRUE`), only biallelic sites will be kept.

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