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Reshape data and classify the haplotypes according to the model

characterize_haplotypes.Rd

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`