LD.filter: Linkage disequilibrium (LD) filter

Description Usage Arguments Details Value Author(s)

View source: R/LD.filter.R

Description

Group SNPs according to their LD.

Usage

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LD.filter(
  genotype.gene,
  tre.mt,
  th = 1,
  tol = 0.05,
  tol.svqtl = 0.25,
  svQTL = FALSE
)

Arguments

genotype.gene

a data.frame with genotype info produced by 'read.bedix'.

tre.mt

a matrix of transcript relative expression (samples x transcripts).

th

r2 threshold over which SNPs will be clustered. Default is 1.

tol

maximum relative difference in sQTL F score allowed to group the SNPs. Default is 0.05.

tol.svqtl

same as tol for svQTL F score. Default is 0.25.

svQTL

should svQTL test be performed. Default is FALSE.

Details

Clusters the SNP IDs of those variants that fulfill the following criteria:

Value

A data.frame with genotype info identical to genotype.gene with an additional column named LD, containing the IDs of the SNPs that fulfill the criteria above and NA otherwise.

Author(s)

Diego Garrido-Martín


guigolab/sQTLseekeR2 documentation built on Nov. 20, 2021, 3:21 a.m.