overlapping_among_groups: Overlapping between grouping factors

In pablobio/GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Description

Takes a dataframe with a column of genes, QTLs (or other data) and a grouping column and create some matrices with the overlapping information

Usage

overlapping_among_groups(file, x, y)

Arguments

file	A dataframe with the data and grouping factor
x	The grouping factor to be compared
y	The data to be compared among the levels of the grouping factor

Value

A list with three matrices: 1) A matrix with the number of overlapping data; 2) A matrix with the percentage of overlapping; 3) A matrix with the combination of the two previous one

Examples

data(QTLmarkers)
data(gtfGenes)
genes.out <- find_genes_qtls_around_markers(db_file=gtfGenes,
marker_file=QTLmarkers,method="gene",
marker="snp",interval=100000, nThreads=1)
overlapping.out<-overlapping_among_groups(
file=genes.out,x="Reference",y="gene_id")

pablobio/GALLO documentation built on March 11, 2021, 2:59 p.m.