balselr

library(balselr)

Read in some data

Read in a vcf ([Variant Call Format][https://en.wikipedia.org/wiki/Variant_Call_Format]) file:

read_vcf(x=system.file("balselr","example.vcf"))

Prepare ncd1 input file

This is an example which shows how to parse a vcf file and output an input file for ncd1:

prep_my_ncd1_file<-parse_vcf(
        infile = system.file(package = "balselr", "example.vcf"),
        n0 = 108,
        type = "ncd1"
)

This is an example which shows how to parse an R object made from a vcf file and output an input file for ncd1:

prep_my_ncd1_file2<-parse_vcf(
        vcf_data = vcf_obj),
        n0 = 108,
        type = "ncd1"
)

Run ncd1 with a 3000 basepair window and a minimum of 8 informative sites per window using 2 cores and a target frequency of 0.5:

res1<-ncd1(x=prep_my_ncd1_file, tf=0.5, w=3000, ncores=2, minIS=8)
res1

Make the minIS filter less restrictive and the window smaller:

res2<-ncd1(x=prep_my_ncd1_file, tf=0.5, w=2000, ncores=2, minIS=2)
res2

Prepare ncd2 input file

This is an example which shows how to parse a vcf file and output an input file for ncd1; use 4 individuals for the outgroup:

prep_my_ncd1_file<-parse_vcf(
        infile = system.file(package = "balselr", "example.vcf"),
        n0 = 108,
        n1 = 4,
        type = "ncd2"
)

This is an example which shows how to parse an R object made from a vcf file and output an input file for ncd1; use only one individual for the outgroup:

prep_my_ncd2_file2<-parse_vcf(
        vcf_data = vcf_obj),
        n0 = 108,
        n1 = 1,
        type = "ncd2"
)

Run ncd2 with a 3000 basepair window and a minimum of 8 informative sites per window using 2 cores and a target frequency of 0.5:

res1<-ncd2(x=prep_my_ncd2_file, tf=0.5, w=3000, ncores=2, minIS=8)
res1

Make the minIS filter less restrictive and the window smaller:

res2<-ncd2(x=prep_my_ncd2_file, tf=0.5, w=2000, ncores=2, minIS=2)
res2