write.ibdhaplo: Write IBDHAPLO

In bowenwang7/r3: Realized Relatedness Estimation and Simulation

Description

write.ibdhaplo prepares the marker data file for running IBDHAPLO.

Usage

write.ibdhaplo(marker, freq, data, member, input.allele = TRUE,
  input.haplotype = FALSE, outfile = tempfile("ibdhaplo", fileext = ".txt"))

Arguments

marker	numeric vector, marker genetic positions in cM.
freq	numeric vector, marker reference allele frequencies.
data	numeric matrix, genetic marker data.
member	string vector, member ID.
input.allele	logical, default TRUE.
input.haplotype	logical, default FALSE.
outfile	string, output file name.

Details

The input marker data needs to be subject/haplotype by marker/allele. For example, suppose data is a 4x10 matrix, use input.allele = FALSE if data contains counts of reference alleles of 4 individuals at 10 markers; use input.haplotype = TRUE if data contains allelic types of 4 haplotypes at 10 markers; use default options if data contains allelic types of 4 individuals at 5 markers.

References

MORGAN Tutorial, https://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml.

Brown et al. (2012) Genetics 190:1447-1460, https://www.ncbi.nlm.nih.gov/pubmed/22298700.

Examples

## Not run: 
nsnp = 7 # number of SNPs
freq = runif(nsnp, 0.05, 0.95)
nhaplo = 4 # number of founder haplotypes
haplotype = sim.haplotype(freq, nhaplo)
marker = sort(runif(7,0,100))
write.ibdhaplo(marker, freq, haplotype, member = c("ind1", "ind2"), 
input.haplotype = TRUE)

## End(Not run)

bowenwang7/r3 documentation built on May 17, 2019, 6:39 p.m.