top_snps: Create table of top snp associations
In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description Usage Arguments See Also Examples

Create a table of the top snp associations

1 2	top_snps(scan1_output, snpinfo, lodcolumn = 1, chr = NULL, drop = 1.5, show_all_snps = TRUE)

`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.

index_snps(), genoprob_to_snpprob(), scan1snps(), plot_snpasso() in R/qtl2plot

## Not run: 
# load example DO data from web
library(qtl2geno)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/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)

# download snp info from web
tmpfile <- tempfile()
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/DOex/c2_snpinfo.rds")
download.file(file, tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)

# calculate strain distribution patterns
snpinfo$sdp <- calc_sdp(snpinfo[,-(1:4)])

# identify groups of equivalent SNPs
snpinfo <- index_snps(DOex$pmap, snpinfo)

# convert to snp probabilities
snppr <- genoprob_to_snpprob(apr, snpinfo)

# perform SNP association analysis (here, ignoring residual kinship)
out_snps <- scan1(snppr, DOex$pheno)

# table with top SNPs
top_snps(out_snps, snpinfo)

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

# top SNPs within 0.5 LOD of max
top_snps(out_snps, snpinfo, 0.5)

## End(Not run)