phyclust (version 0.1-34)

data.phylip.crohn: Crohn's Disease SNP Dataset in the phylip Format

Description

Crohn's disease dataset is published by Hugot, et al. (2001).

Format

A text file in phylip format is stored in the data subdirectory.

Author

Hugot, J.P., et al. (2001).

Details

Crohn's disease dataset is used to perform haplotype grouping used in Tzeng's paper (2005).

Totally, 1102 haplotypes/SNP sequences and 8 sites.

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

Hugot, J.P., et al. (2001) “Association of NOD2 Leucine-Rich Repeat Variants with Susceptibility to Crohn's Disease”, Nature, 411, 599-603.

Tzeng, J.Y. (2005) “Evolutionary-Based Grouping of Haplotypes in Association Analysis”, Genetics Epidemiology, 28, 220-231. https://www4.stat.ncsu.edu/~jytzeng/software.php

See Also

read.phylip.

Examples

if (FALSE) {
library(phyclust, quiet = TRUE)

data.path <- paste(.libPaths()[1], "/phyclust/data/crohn.phy", sep = "")
# edit(file = data.path)
my.snp <- read.phylip(data.path, code.type = "SNP")
str(my.snp)
}