find_genes_qtls_around_markers: Search genes and QTLs around candidate regions

Description Usage Arguments Value Examples

View source: R/find_genes_qtls_around_markers.R

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

1
2
3
4
5
6
7
8
9
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

1
2
3
4
5
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)

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