sdp_to_pattern: Convert sdp to pattern

In byandell/qtl2pattern: Pattern Support for 'qtl2' Package

Convert sdp to pattern

Description

Convert strain distribution pattern (sdp) to letter pattern.

Usage

sdp_to_pattern(sdp, haplos, symmetric = TRUE)

sdp_to_logical(sdp, haplos, symmetric = TRUE)

Arguments

sdp	vector of sdp values
haplos	letter codes for haplotypes (required)
symmetric	make patterns symmetric if TRUE

Value

vector of letter patterns

Author(s)

Brian S Yandell, [e-mail]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"


# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Extract strain distribution pattern.
sdp <- snpinfo$sdp
# Find out how many alleles.
nallele <- ceiling(log2(max(sdp)))
out <- sdp_to_pattern(sdp, LETTERS[seq_len(nallele)])
# Show most frequent patterns. 
head(rev(sort(c(table(out)))))

byandell/qtl2pattern documentation built on Nov. 9, 2023, 7:57 p.m.