Find Synteny Blocks

Description

Creates synteny blocks from homeolog positions. See the vignette for more information.

Usage

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find_blocks(df, eps = 2000000L, minPts = 100L, minLength = 1000000L,
  maxLength = 10000000L, gap = 0L)

Arguments

df

Data frame with positions.

eps

Numeric, eps parameter for dbscan

minPts

Integer, minPTS parameter for dbscan.

minLength

Integer, minimal block length. Blocks below this threshold will be filtered out.

maxLength

Integer, maximal block length. Blocks above this threshold will be split up.

gap

Numeric, gap size between chromosomes.