top_snps: Create table of top snp associations
In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

top_snps

R Documentation

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
)

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.

Value

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

Examples

## Not run: 
# 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)

## End(Not run)

qtl2 documentation built on May 29, 2024, 11:46 a.m.