dot-fixRotation: Fix strand label rotation across consecutive block-structure...

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Fix strand label rotation across consecutive block-structure columns

Description

Internal helper to enforce a consistent strand-label orientation across adjacent columns of a block-structure matrix.

Usage

.fixRotation(blockStructure)

Arguments

blockStructure

A numeric matrix (typically individuals in rows, SNPs in columns) representing a block/strand structure. Values are expected to be small integers (commonly including '0', '1', '2' and possibly other internal codes).

Details

The input typically encodes sire strand-of-origin labels per individual (rows) and marker/SNP (columns), where '0' indicates unknown and non-zero values indicate an assigned strand/state. The native algorithm compares each column to the previous one and, when a "contrast" (swap of strand labels) increases agreement, it relabels the next column to reduce apparent strand-rotation between columns.

This function is a thin R wrapper around the native routine fixRotation implemented in C++ and called via .Call().

At each step, the C++ code computes an agreement score between column i and column i+1 using only positions where both columns are non-zero. It also computes the score after applying a contrast mapping to column i+1 (conceptually swapping strand labels '1' and '2', leaving '0' unchanged). If the contrasted version agrees more with column i, the function relabels column i+1.

The relabeling performed by the native code is:

• '1 -> 3'

• '2 -> 1'

• '3 -> 2'

leaving other values unchanged. (These codes are part of hsphase's internal block/strand encoding.)

Value

A numeric matrix with the same dimensions as blockStructure, where some entries in column i+1 may be relabeled to improve consistency with column i. The transformation is applied iteratively from left to right across columns.

See Also

bmh, ssp, aio for creation and downstream usage of block structures.

hsphase documentation built on Feb. 17, 2026, 5:07 p.m.