inst/shiny/help/settings.md

In KLINK: Kinship Analysis with Linked Markers

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Settings

Marker map

The marker map specifies the genetic positions of markers, measured in centiMorgans (cM).

• Built-in: A map with updated positions for 50 markers from several common forensic STR kits. (Default.)
• Custom: Lets you upload your own map file.

A custom map file must be tab-delimited and contain columns matching Marker, Chr, and cM. Column order does not matter, and matching is case-insensitive. Longer names are also accepted, provided they start with matching terms; for example Marker name or Chromosome. If no column matches cM, KLINK will look for POS instead and use that column as the marker position.

Chromosome values must be positive integers, optionally written with the prefix chr.

Map function

Controls how recombination fractions are derived from genetic distances.

• Kosambi: Allows for crossover interference. (Default.)
• Haldane: Assumes no crossover interference.

In most cases, the choice has only a modest effect. If in doubt, use Kosambi.

Mutation model

Controls how mutations are modelled in the likelihood calculations.

• Original: Uses the mutation model specified in the input file. (Default.)
• Simple: Applies an 'equal' model with rate 0.001, to all markers.
• Off: Disables all mutation models.

The main purpose of the Simple option is to provide a lightweight fallback when the input file lacks mutation models. Off is intended mainly for testing. Note that the LR table always includes a 'No mut' column, regardless of this setting.

Empty markers

Controls whether markers without genotype data are shown in the tables.

• Hide: Omit empty markers. (Default.)
• Show: Include them in the tables.

Affects both app display and downloaded tables.

Likelihoods

Controls whether (log-)likelihood columns are included in the LR table.

• Hide: Show LR columns only. (Default.)
• Show: Show likelihood columns.
• Loglik: Show log-likelihood columns.

Affects app display only; both likelihoods and log-likelihoods are always included in the 'LR table' sheet of the Excel download.

Decimals

Number of decimals shown in tables. Affects app display only; downloaded results use full precision.

Unlinked > cM

Markers farther apart than this threshold are treated as unlinked. Leave this empty to indicate no limit (this is the default), meaning that markers on the same chromosome are always linked.

KLINK documentation built on April 21, 2026, 5:10 p.m.