Genomic Annotation in Livestock for Positional Candidate LOci
Sub-function to auto-stop the clusters created for parallel processes
Run a short EM on p-values to fit a 2-component Beta mixture
Search genes and QTLs around candidate regions
Function to annotate markers and the respective p-values within genes
Function to estimate the posterior probability of association (PPA) ba...
Estimate a gene-level p-value using Weighted Z-score approach, Meta-an...
Global variables
Import .gtf and .gff files to be used during gene and QTL annotation, ...
Compute the eigenvalues for the linkage disequilibrium (LD) matrix and...
Function to compute the weighted 1-dimensional kernel density estimato...
Function to estimate gene-level p-value using Davies algorithm
Function to perform Meta-Analysis with LD Correlation Coefficients
Function to perform an EM algorithm (logistic prior ...
Function to perform an EM algorithm (“Multiple” univariate KDEs (nonpa...
Function to perform an EM algorithm (multivariate normal with shared c...
Function to perform an EM algorithm (Gaussian naive Bayes (parametric,...
Function to perform an EM algorithm (LDA projection + 1D KDE (nonparam...
Network Embedding using biased random walk and Word2Vec.
Compute the centrality metrics for the nodes composing the network gen...
Create a dynamic network representing the relationship between two gro...
Estimate the number of effective markers in a chromosome based on an a...
Estimate the number of independent segments in a chromosome based on t...
Overlapping between grouping factors
Compute Meff statistic based on PCA to determine the number of effecti...
Compute a multi-trait test statistic for pleiotropic effects using sum...
Plot overlapping between data and grouping factors
Plot QTLs information from the find_genes_qtls_around_markers output
Performs a QTL enrichment analysis based on a hypergeometric test for ...
Plot enrichment results for QTL enrichment analysis
Plot relationship between data and grouping factors
Function to performs a linear discriminant analysis (LDA) for a multiv...
Sub-function to split comment column from QTL output
Sub-function to search genes around candidate markers
Sub-function to search genes around candidate markers
Sub-function to search QTLs around candidate markers
Sub-function to search QTLs around candidate markers
Performs a QTL enrichment analysis based in a Bootstrap simulation for...
Performs a QTL enrichment analysis based in a Bootstrap simulation for...
Function to perform Weighted Z-score Approach with LD Information
The accurate annotation of genes and Quantitative Trait Loci (QTLs) located within candidate markers and/or regions (haplotypes, windows, CNVs, etc) is a crucial step the most common genomic analyses performed in livestock, such as Genome-Wide Association Studies or transcriptomics. The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an intuitive and straightforward environment to annotate positional candidate genes and QTLs from high-throughput genetic studies in livestock. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chicken, among others.