sub_qtlEnrich_geno: Performs a QTL enrichment analysis based in a Bootstrap...

In GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Performs a QTL enrichment analysis based in a Bootstrap simulation for each QTL class using the QTL information across the whole genome

Description

Takes the output from find_genes_qtls_around_markers and run a QTL enrichment analysis

Usage

sub_qtlEnrich_geno(
  qtl_file,
  qtl_type,
  qtl.file.types,
  table.qtl.class,
  padj,
  qtl_db,
  search_qtl,
  nThreads
)

Arguments

qtl_file	The output from find_genes_qtls_around_markers function
qtl_type	A string indicating with QTL enrichment will be performed: "QTL_type" or "Name"
qtl.file.types	A vector with the observed QTL classes
table.qtl.class	An frequency table for the number of each QTL in each chromosome
qtl_db	The QTL annotation database
search_qtl	The column to perform the QTL searching in counting from the QTL annotation database
nThreads	Number of threads for parallel processing

Value

A data frame with the p-value for th enrichment result

GALLO documentation built on June 22, 2024, 9:17 a.m.