daeqtl_mapping: DAEQTL mapping

In maialab/daeqtlr: DAEQTL Mapping

DAEQTL mapping

Description

TODO

Usage

daeqtl_mapping(
  snp_pairs,
  zygosity,
  ae,
  fn = daeqtl_test,
  ...,
  .extra_cols = 2L,
  .n_chunks = future::nbrOfWorkers()
)

Arguments

snp_pairs	A data frame with DAE SNP/candidate SNP pairs.
zygosity	A data frame with zygosity levels of samples. First column should be the SNP identity, and remaining columns should refer to biological samples. These should be factors, and their levels should be "hom" (homozygous) and "het" (heterozygous).
ae	A data frame with allelic expression (AE) ratios. Each row is for a locus. The locus identity is indicated in the first column. Remaining columns are samples.
fn	A function implementing the statistical association approach. This function needs to have two named arguments ae_hom and ae_het. Extra arguments will be read from ....
...	Extra arguments passed on to the call of the function passed in fn.
.extra_cols	The number of extra columns you are creating with fn.
.n_chunks	The number of chunks to divide snp_pairs for parallel processing. If you are going to run in parallel set this number to be equal to the total number of workers.

Value

An updated version of the data frame snp_pairs. The update includes extra columns, typically pvalue and case.

maialab/daeqtlr documentation built on May 18, 2022, 6:53 a.m.