find_genes_qtls_around_markers {GALLO}

Search genes and QTLs around candidate regions

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 data frame 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 columns 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)