Description Usage Arguments Details Value Author(s) References See Also
View source: R/functions-SNP_time_series.R
This function initializes a genome-wide time series data set that can be used as input for haplotype-block reconstruction.
1 2 3 4 | 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)
|
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 |
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 |
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. |
The function takes as input genome-wide frequencies of SNPs polarized for the minor frequency allele
in the experimnetal starting population for multiple time points and replicates. SNP positions are filtered for a
maximum frequency in the experimental starting population and a minimum frequency change in at least one time point
for a specified number of replicates. The initialized data is returned as a SNP_time_series object that is
required as input for the function reconstruct_hb
to reconstruct unknown haplotype-blocks from the experimental
starting population.
an object of the class SNP_time_series
data
Susanne U. Franssen
Franssen, Barton & Schloetterer 2016, Reconstruction of haplotype-blocks selected during experimental evolution, MBE
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