RILStEp(Recombinant Inbred Lines Stepwise Epistasis analysis) package is
the epistasis analysis tool. This package enables to detect the
epistatic relationships between SNPs for RIL population by comparison of
2 models based on bayes factor.
publication:
https://doi.org/10.1093/g3journal/jkab130
Other than CRAN package, GWASpoly package is required for RILStEp
package.
please install it.
install.packages("devtools")
devtools::install_github("jendelman/GWASpoly", build_vignettes=FALSE)You can install RILStEp from GitHub with:
# install.packages("devtools")
devtools::install_github("slt666666/RILStEp")This is a basic example script:
library(RILStEp)
### loading dataset
loaded_data <- load_data("phenotype.csv", "genotype.csv", "trait1")
### check all combinations of 2 SNPs
result1 <- rilstep(loaded_data, "result1", core_num = 8)
### using 1 SNP in each 500 SNPs
result2 <- rilstep(loaded_data, "result2", interval = 500)
### specify QTL-like SNPs by user.
result3 <- rilstep(loaded_data, "result3", qtls = c("chr08_19928351", "chr09_3909046"))
### specify No QTLs.
result4 <- rilstep(loaded_data, "result3", qtls = FALSE)
### using SNPs in specific regions
result5 <- rilstep(loaded_data, "result4", region = c("chr03_2132221:chr10_9330401", "chr03_2132221:chr10_9330401"))
### consider heterozygous
result6 <- rilstep(loaded_data, "result5", heterozygous = TRUE)
### example
result7 <- rilstep(loaded_data, "result6", interval = 500, region = c("chr03_2132221:chr10_9330401", "chr03_2132221:chr10_9330401"), core_num = 8)option region=c() can specify regions. rilstep check all combinations
of SNPs in specified
regions.
region = c("chr03_1234") # chr03_1234 x all SNPs
region = c("chr03_1234:chr10_5678") # chr03_1234 ~ chr10_5678 x all SNPs
region = c("chr03_1234", "chr10_5678") # chr03_1234 x chr10_5678
region = c("chr03_1234:chr10_5678", "chr04_9012:chr7_3456") # chr03_1234~chr10_5678 x chr04_9012~chr7_3456
input files should be csv format.
phenotype data
| Name | trait1 |
|---|---|
| Sample1 | 12.3 |
| Sample2 | 23.4 |
| … | … |
| SampleXX | 78.9 |
genotype data
| Marker | Chrom | Position | Sample1 | Sample2 | … | SampleXX |
|---|---|---|---|---|---|---|
| 1 | chr01 | 1234 | 2 | 2 | … | 2 |
| 2 | chr01 | 3456 | 2 | 0 | … | 0 |
| 3 | chr01 | 9999 | 0 | 0 | … | 1 |
| … | … | … | … | … | … | |
| XXX | chr12 | 4869786 | 0 | 0 | … | 2 |
marker coded as {0,1,2} = {AA,AB,BB}
A, B: each parental
genotype
!! Only bi-allelic markers are allowed !!