Usage
initialize_SNP_time_series(chr, pos, base.freq, lib.freqs, pop.ident, pop.generation, use.libs, minfreqchange = 0.2, minrepl = 3, max.minor.freq = 3/200, winsize = 5e+05, min.minor.freq = 0, min.lib.frac = 0.75, win.scale = "bp", pos.cM = NULL)
Arguments
chr
character vector specifying the chromosome name for each genome-wide SNP
pos
numeric vector specifying the chromosomal position for each genome-wide SNP
base.freq
numeric vector specifying the frequency of the minor allele polarized in experimental
starting population for each genome-wide SNP
lib.freqs
matrix specifying the frequencies of all genome-wide SNPs (rows) for all different libraries
(time points and replicates, columns).
pop.ident
numeric vector specifying the identity of each library in terms of replicate ID
pop.generation
numeric vector specifying the time point of the respective library
use.libs
logical vector specifying which libraries should be used for haplotype-block
reconstruction. The choice taken here determines SNP filtering as parameters minfreqchange
and minrepl depend on the choice of the data set here. For visualization of marker frequencies,
however, the remaining libraries will also be available.
minfreqchange
numeric specifying the minimum frequency change required in 'minrepl' replicates required to
include the SNP in the analysis
minrepl
numeric specifying the number of replicates, in which the 'minfreqchange' is required to include
the SNP in the analysis
max.minor.freq
numeric specifying the maximum frequency of the minor allele (polarized in the
experimental starting population) to be included in the analysis
winsize
numeric specifying the window size on which to perform the analysis
min.minor.freq
numeric specifying the minimum frequency of the minor allele (polarized in the
experimental starting population) to be included in the analysis (default=0).
min.lib.frac
minimum fraction of non-NA values for a SNP across
libraries (only using libraries specified in use.libs) (default=0.75).
win.scale
character string specifying which genome-wide distance
measure is used for window definition. Options are "bp" (base pairs) or
"cM" (centi Morgan). cM distances can only be used if gentic positions are
provided in 'pos.cM' (default="Mb").
pos.cM
numeric vector corresponding to SNP positions in col.info with
genetic positions in cM.