Description Usage Arguments Details Value
tajimas_d
uses the PopGenome package to calculate Tajima's D across an interval.
1 2 3 4 5 | tajimas_d(vcf_path = paste0(path.package("cegwas"), "/"),
vcf_name = paste0("WI.", vcf_version, ".impute.vcf.gz"),
chromosome = "II", interval_start = 11021073, interval_end = 12008179,
window_size = 300, slide_distance = 100, samples = colnames(snps[,
5:ncol(snps)]), outgroup = "N2", site_of_interest = 11875145)
|
vcf_path |
character value of the directory path where tabix-indexed VCF file is |
vcf_name |
character value corresponding to tabix-indexed VCF file name |
chromosome |
character value corresponding to chromosome of interest. This should be the same chromosome name that is present in the VCF file |
interval_start |
numeric value start of interval of interest |
interval_end |
numeric value end of interval of interest |
window_size |
size of window to calculate Tajima's D in SNPs (default = 300) |
slide_distance |
number of SNPs to shift window (default = 100) |
samples |
character vector of strains to use for analysis (default is 152 strain list present in cegwas package) |
outgroup |
character value corresponding to strain (or strains) to serve as reference (default value is "N2") |
site_of_interest |
numeric value, if specified adds a line to the plot at this position. |
This is the detail section if you want to fill out in the future
Outputs a list, where the first element is a dataframe containing Tajima's D calculations and the second is a ggplot2 object visualizing Tajima's D across the interval
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