data.phylip.crohn | R Documentation |
Crohn's disease dataset is published by Hugot, et al. (2001).
A text file in phylip format is stored in the data subdirectory.
Crohn's disease dataset is used to perform haplotype grouping used in Tzeng's paper (2005).
Totally, 1102 haplotypes/SNP sequences and 8 sites.
Hugot, J.P., et al. (2001).
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
read.phylip
.
## Not run:
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)
## End(Not run)
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