evalPL: Evaluate evidence of physical linkage for positive...

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Evaluate evidence of physical linkage for positive associations with summary statistics of distance measurements

Description

This function evaluates evidence of physical linkage using association status and consistency in allelic physical distances.

Usage

evalPL(
  lmms,
  min.beta = 0,
  max.p = 0.05,
  max.range = 2000,
  min.pIBD = 0.9,
  score.dist = FALSE
)

Arguments

lmms	This argument can be a list produced by the function summariseDist, which contains LMM parameters and distance measurements. It can also be the data frame assoc in the output of findPhysLink or lmms in the output of function lmm. When the latter two kinds of input are used, users can rescore the evidence using new criteria.
min.beta	only associations with beta's >= min.beta will be considered as showing evidence of physical linkage.
max.p	only associations with P values <= max.p will be considered as signficant.
max.range	An integer specifying the maximum range (in bp) of in-group allelic physical distances allowed to call consistent.
min.pIBD	(optional) Minimum probability of the root of a minimum inclusive clade to display a positive binary trait, such as having a pair of alleles co-occurring or a specific allelic physical distance. Default: 0.9 (90%).
score.dist	(optional) A logical parameter specifying whether allelic physical distances should be taken into account for scoring edges. Default: FALSE.

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.