find_genes_qtls_around_markers: Search genes and QTLs around candidate regions

In GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Description

Takes a list of candidate markers and or regions (haplotypes, CNVs, windows, etc.) and search for genes or QTLs in a determined interval

Usage

find_genes_qtls_around_markers(
  db_file,
  marker_file,
  method = c("gene", "qtl"),
  marker = c("snp", "haplotype"),
  interval = 0,
  nThreads = NULL,
  verbose = TRUE
)

Arguments

db_file	The dataframe obtained using the import_gff_gtf() function
marker_file	The file with the SNP or haplotype positions. Detail: For SNP files, the columns “CHR” and “BP” with the chromosome and base pair position, respectively, are mandatory. For the haplotype, the following collumns are mandatory: “CHR”, “BP1” and “BP2”
method	“gene” or “qtl”
marker	"snp" or "haplotype"
interval	The interval in base pair which can be included upstream and downstream from the markers or haplotype coordinates.
nThreads	Number of threads to be used
verbose	Logical value defining if messages should of not be printed during the analysis (default=TRUE)

Value

A dataframe with the genes or QTLs mapped within the specified intervals

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)

GALLO documentation built on Nov. 10, 2021, 1:07 a.m.