iterate_conditional_celltypes: iterate_conditional_celltypes

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

iterate_conditional_celltypes

Description

Support function for calculate_conditional_celltype_associations.

Usage

iterate_conditional_celltypes(
  ctd,
  EnrichmentMode,
  signifCells2,
  annotLevel,
  controlledAnnotLevel,
  genesCovarFile,
  controlCovarFile,
  controlledCovarCols,
  magmaPaths,
  upstream_kb,
  downstream_kb,
  version,
  verbose
)

Arguments

ctd	Cell type data structure containing specificity_quantiles.
EnrichmentMode	[Optional] Should either 'Linear' or 'Top 10%' mode be used for testing enrichment?
controlledAnnotLevel	Which annotation level should be controlled for.
upstream_kb	How many kb upstream of the gene should SNPs be included?
downstream_kb	How many kb downstream of the gene should SNPs be included?
version	MAGMA version to use.
verbose	Print messages.

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.