gigwa_get_variants: Get variants in the selected GIGWA run

In khaled-alshamaa/QBMS: Query the Breeding Management System(s)

Get variants in the selected GIGWA run

Description

Query the variants (e.g., SNPs markers) in the selected GIGWA run that match a given criteria.

Usage

gigwa_get_variants(
  max_missing = 1,
  min_maf = 0,
  samples = NULL,
  start = NULL,
  end = NULL,
  referenceName = NULL
)

Arguments

max_missing	maximum missing ratio (by sample) between 0 and 1 (default is 1 for 100%).
min_maf	minimum Minor Allele Frequency (MAF) between 0 and 1 (default is 0 for 0%).
samples	a list of a samples subset (default is NULL will retrieve for all samples).
start	start position of region (zero-based, inclusive) (e.g., 19750802).
end	end position of region (zero-based, exclusive) (e.g., 19850125).
referenceName	reference sequence name (e.g., '6H' in the Barley LI-AM).

Value

A data.frame that has the first 4 columns describe attributes of the SNP (rs#: variant name, alleles: reference allele / alternative allele, chrom: chromosome name, and pos: position in bp), while the following columns describe the SNP value for a single sample line using numerical coding 0, 1, and 2 for reference, heterozygous, and alternative/minor alleles.

Author(s)

Khaled Al-Shamaa, [e-mail]

Examples

if(interactive()) {
# config your GIGWA connection
set_qbms_config("https://gigwa.southgreen.fr/gigwa/", 
                time_out = 300, engine = "gigwa", no_auth = TRUE)

# select a database by name
gigwa_set_db("Sorghum-JGI_v1")

# select a project by name
gigwa_set_project("Nelson_et_al_2011")

# select a specific run by name
gigwa_set_run("run1")

marker_matrix <- gigwa_get_variants(max_missing = 0.2, 
                                    min_maf = 0.35, 
                                    samples = c("ind1", "ind3", "ind7"))
}

khaled-alshamaa/QBMS documentation built on Jan. 27, 2024, 6:40 a.m.