characterize_haplotypes: Reshape data and classify the haplotypes according to the...

In jeinson/tompen: [Sta]tistics for [M]odified [Pen]etrance

Reshape data and classify the haplotypes according to the model

Description

This function takes the haplotype configurations in the standard input format and reshapes them for more intuitive processing. See the sample dataset

Usage

characterize_haplotypes(
  dataset,
  beta_config,
  qtl_allele_frequency_column = "qtl_af",
  gene_name_column = "gene"
)

Arguments

dataset	A data.frame or tibble. The input dataset. See sample data for format
beta_config	Vector. The values assigned to beta for each haplotype possibility. This can be changed to tweak the hypothesis. Values are provided in the package as 'beta_config_eqtl' and 'beta_config_sqtl', depending on the hypothesis you are testing.
qtl_allele_frequency_column	String. The name of the column in the input data with QTL allele frequencies. Default: 'sqtl_af' the modified penetrance hypothesis.
gene_name_column	String. The name of the column in the input data with the gene name. Default: 'gene'

jeinson/tompen documentation built on March 18, 2023, 2:59 a.m.