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Determine significant and suggestive LOD thresholds

LOD_thld.Rd

Determine significant and suggestive LOD thresholds for your QTLs, using scan1perm from qtl2. Select the number of genes to permute, the number of permutations, and the number of genes to run in each batch.

Usage

LOD_thld(
  mapping,
  tissue,
  annots = NULL,
  n.gene = 75,
  n.perm = 750,
  batch.size = 5
)

Arguments

mapping

Mapping list from mapQTL, or full path to .rds containing one.

tissue

Tissue to determine thresholds for.

annots

Data frame of phenotype annotations for filtering to autosomal phenotypes. Columns must include "id", "symbol", "start", "end".

n.gene

Number of phenotypes to run permutations on. Default is 75.

n.perm

Number of permutations to run per phenotype. Default is 750.

batch.size

Number of genes in each parallelized batch.

Value

A list containing:

perms

A scan1perm object of permutations for all selected genes.

thresholds

A list with two elements:

significant

Median LOD threshold at alpha = 0.05.

suggestive

Median LOD threshold at alpha = 0.4.