README.md

In slt666666/RILStEp: What the Package Does (One Line, Title Case)

RILStEp

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

Requirements

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)

Installation

You can install RILStEp from GitHub with:

# install.packages("devtools")
devtools::install_github("slt666666/RILStEp")

Example

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 data format

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 !!

slt666666/RILStEp documentation built on Feb. 23, 2022, 1:04 a.m.