qtl2 (version 0.32)

top_snps: Create table of top snp associations

Description

Create a table of the top snp associations

Usage

top_snps(
  scan1_output,
  snpinfo,
  lodcolumn = 1,
  chr = NULL,
  drop = 1.5,
  show_all_snps = TRUE
)

Value

Data frame like the input snpinfo with just the selected subset of rows, and with an added column with the LOD score.

Arguments

scan1_output

Output of scan1(). Should contain a component "snpinfo", as when scan1() is run with SNP probabilities produced by genoprob_to_snpprob().

snpinfo

Data frame with SNP information with the following columns (the last three are generally derived with index_snps()):

• chr - Character string or factor with chromosome

• pos - Position (in same units as in the "map" attribute in genoprobs.

• sdp - Strain distribution pattern: an integer, between 1 and \(2^n - 2\) where \(n\) is the number of strains, whose binary encoding indicates the founder genotypes

• snp - Character string with SNP identifier (if missing, the rownames are used).

• index - Indices that indicate equivalent groups of SNPs, calculated by index_snps().

• intervals - Indexes that indicate which marker intervals the SNPs reside.

• on_map - Indicate whether SNP coincides with a marker in the genoprobs

lodcolumn

Selected LOD score column to (a numeric index, or a character string for a column name). Only one value allowed.

chr

Selected chromosome; only one value allowed.

drop

Show all SNPs with LOD score within this amount of the maximum SNP association.

show_all_snps

If TRUE, expand to show all SNPs.

See Also

index_snps(), genoprob_to_snpprob(), scan1snps(), plot_snpasso()

Examples

if (FALSE) {
# load example DO data from web
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)

# subset to chr 2
DOex <- DOex[,"2"]

# calculate genotype probabilities and convert to allele probabilities
pr <- calc_genoprob(DOex, error_prob=0.002)
apr <- genoprob_to_alleleprob(pr)

# query function for grabbing info about variants in region
dbfile <- system.file("extdata", "cc_variants_small.sqlite", package="qtl2")
query_variants <- create_variant_query_func(dbfile)

# SNP association scan, keep information on all SNPs
out_snps <- scan1snps(apr, DOex$pmap, DOex$pheno, query_func=query_variants,
                      chr=2, start=97, end=98, keep_all_snps=TRUE)

# table with top SNPs
top_snps(out_snps$lod, out_snps$snpinfo)

# top SNPs among the distinct subset at which calculations were performed
top_snps(out_snps$lod, out_snps$snpinfo, show_all_snps=FALSE)

# top SNPs within 0.5 LOD of max
top_snps(out_snps$lod, out_snps$snpinfo, drop=0.5)
}