LD.filter: Linkage disequilibrium (LD) filter

In guigolab/sQTLseekeR2: R package for splicing QTL mapping

Description

Group SNPs according to their LD.

Usage

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:

• LD (r2) >= th.

• Relative differences in sQTL F score <= tol

• Relative differences in svQTL F score <= tol.svqtl (if svQTL is TRUE)

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.