QTLenrich_plot: Plot enrichment results for QTL enrichment analysis

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

Description

Takes the output from qtl_enrich function and creates a bubble plot with enrichment results

Usage

QTLenrich_plot(qtl_enrich, x, pval)

Arguments

qtl_enrich	The output from qtl_enrich function
x	Id column to be used from the qtl_enrich output
pval	P-value to be used in the plot. The name informed to this argument must match the p-value column name in the enrichment table

Value

A plot with the QTL enrichment results

Examples

data(QTLmarkers)
data(gffQTLs)
out.qtls<-find_genes_qtls_around_markers(db_file=gffQTLs,
marker_file=QTLmarkers, method = "qtl",
marker = "snp", interval = 500000,
nThreads = 1)

out.enrich<-qtl_enrich(qtl_db=gffQTLs,
qtl_file=out.qtls, qtl_type = "Name",
enrich_type = "genome", chr.subset = NULL, padj = "fdr",nThreads = 1)

out.enrich.filtered<-out.enrich[which(out.enrich$adj.pval<0.05),]
QTLenrich_plot(out.enrich.filtered, x="QTL", pval="adj.pval")

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