SNP_time_series-class: An S4 class storing time series data
In haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

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An S4 class representing the input data for haplotype-block reconstruction

Time-series data is initialzed to be used for haplotype-block reconstruction.

An S4 class storing the initialized input data for haplotype-block reconstruction with reconstruct_hb. Genome-wide time series data for multiple time points and replicates is stored along with replicate and time point information of the time series data. The stored data is filtered for SNPs with a maximum minor frequency in the experimental starting population and a minimum frequency change minfreqchange that is required for minrepl many replicates. An object of the class SNP_time_series can only be created with the function initialize_SNP_time_series.

col.info: data.table with columns 'chr', 'pos', 'base.freq' and window. Each row corresponds to a SNP position that fullfills the filtering criteria.
lib.freqs: data.table with columns for the different libraries (time points and replicates) and rows for all SNP positions that fullfill the filtering criteria.
pos.cM: numeric vector corresponding to SNP positions in col.info with genetic positions in cM.
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
winsize: numeric specifying the window size on which to perform the analysis
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").
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).
max.minor.freq: numeric specifying the maximum frequency of the minor allele (polarized in the experimental starting population) to be included in the analysis (default=3/113).
min.lib.frac: minimum fraction of non-NA values for a SNP across libraries (only using libraries specified in use.libs) (default=0.75).
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