tss_tts.calc: calculate minor allele frequencies of polymorphisms in...

In greymonroe/polymorphology: Functions from Monroe et al 2022

calculate minor allele frequencies of polymorphisms in relation to gene bodies

Description

calculate minor allele frequencies of polymorphisms in relation to gene bodies

Usage

tss_tts.calc(
  gff,
  vcf,
  type = "both",
  chrs = "all",
  num = "all",
  feature = "gene",
  variable
)

Arguments

gff	directory and file name of reference gff OR data.table object of gff data
vcf	directory and file name vcf data OR data.table object of variant data (data.table with CHROM, POS, MAF)
type	"snp", "indel", or "both", default is "both"
chrs	selection specific chromosomes, default is "all"
num	set number of genes, default is "all
feature	name of the feature in the gff data that you want to look at, default is "gene"
variable	name of variable in the vcf you want the calculated value of in relation to TSS TTS

Value

a vector of the relative position of polymorphsims in relation to feature

greymonroe/polymorphology documentation built on Aug. 6, 2023, 1:33 a.m.