# Genomic Annotation in Livestock for Positional Candidate LOci

## Documentation for package ‘GALLO’ version 2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

find_genes_qtls_around_markers | Search genes and QTLs around candidate regions
Gene_PPA | Function to estimate the posterior probability of association (PPA) based on the integration of -OMICs and functional data via representation learning of candidate genes.
gene_pval | Estimate a gene-level p-value using Weighted Z-score approach, Meta-analysis with LD correlation coefficients approach, and Davies algorithm
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
Net_embedding | Network Embedding using biased random walk and Word2Vec.
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