iterate_conditional_celltypes_grouped: iterate_conditional_celltypes: grouped

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

iterate_conditional_celltypes: grouped

Description

Support function for calculate_conditional_celltype_associations.

Usage

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

Arguments

allRes	Results from MAGMA.Celltyping::iterate_conditional_celltypes.
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 Aug. 21, 2023, 8:55 a.m.