hbr-class: An S4 class storing results from haplotype-block...
In haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

Description Details Slots Author(s) References See Also

An S4 class containg input parameters and results for reconstructed haplotype-blocks

An S4 class containing a SNP_time_series data object, the haplotype-blocks were constructed on, parameters that were used for haplotype-block reconstruction and results of haplotype block reconstruction. An hbr object can only be created with reconstruct_hb.

dat: A SNP_time_series object containg the time series data and threshold used for marker filtering (refer to SNP_time_series for more details)
chromosome: The chromosome for which haplotype-blocks were calculated.
min.cl.size: Numeric specifying the minimum number of correlated markers in a window for haplotype-block reconstruction
min.cl.cor: Numeric specifying the correlation between marker SNPs required using average linkage clustering for markers to be assembled in one cluster
min.inter: Numeric specifying the minimum number of markers in two clusters of overlapping windows required to be identical for cluster elongation across windows to build haplotype-blocks
single.win: Boolean specifying that are supported by only a cluster in one window are also included in the markers of reconstructed blocks. If FALSE only hbrs are returned that span at least two windows and only markers being present in the intersection between overlapping windows are included.
transf: Boolean indicating if time series data was sqrt transformed prior to clustering.
scaleSNP: Boolean indicating if time series data was scaled (mean=0, var=1) for each SNP prior to clustering.
pos.cor: Boolean indicating if negative correletions between time series between two SNPs were set to zero prior to clustering.
cl.chr: A list containing results from clustering of low frequency markers in the experimental starting population for each window. Each list element contains the results for a window.If clusters for the respective window were identified the respective list numeric vectors with the marker positions for each cluster. If no clusters were identified the list is empty. The clusters identified for overlapping windows are the basis for cluster elongation to haplotype-blocks as present in cl.long.m.
cl.long.m: A list containing the results of haplotype-bock reconstruction. Each list element corresponds to a reconstructed #' haplotype-block and contains a numeric vector with all the SNP positions. The minor allele in the experimnental starting population at those positions represent marker alleles for the respective hapltotype-block. Chromosome-wide haplotype-blocks can be visualized with plot.