Genomic Annotation in Livestock for Positional Candidate LOci

Documentation for package ‘GALLO’ version 1.5

find_genes_qtls_around_markers	Search genes and QTLs around candidate regions
gene_pval	Estimate a gene-level p-value using Weighted Z-score approach and Meta-analysis with LD correlation coefficients approach
import_gff_gtf	Import .gtf and .gff files to be used during gene and QTL annotation, respectively
NetCen	Compute the centrality metrics for the nodes composing the network generated by the NetVis function
NetVis	Create a dynamic network representing the relationship between two groups of variables
Nmarkers_SimpleM	Estimate the number of effective markers in a chromosome based on an adapted version of the simpleM methodology
Nseg_chr	Estimate the number of independent segments in a chromosome based on the effective population size
overlapping_among_groups	Overlapping between grouping factors
PleioChiTest	Compute a multi-trait test statistic for pleiotropic effects using summary statistics from association tests
plot_overlapping	Plot overlapping between data and grouping factors
plot_qtl_info	Plot QTLs information from the find_genes_qtls_around_markers output
QTLenrich_plot	Plot enrichment results for QTL enrichment analysis
qtl_enrich	Performs a QTL enrichment analysis based on a hypergeometric test for each QTL class
relationship_plot	Plot relationship between data and grouping factors