load_magma_results_file: Load a MAGMA .gcov.out file

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

Load a MAGMA .gcov.out file

Description

Convenience function which just does a little formatting to make it easier to use.

Usage

load_magma_results_file(
  path,
  ctd,
  annotLevel,
  EnrichmentMode,
  genesOutCOND = NA,
  analysis_name = NULL,
  ControlForCT = "BASELINE",
  keep_all_rows = FALSE,
  verbose = TRUE
)

Arguments

path	Path to a .gcov.out file (if EnrichmentMode=='Linear'). or .sets.out (if EnrichmentMode=='Top 10%').
ctd	Cell type data structure containing specificity_quantiles.
annotLevel	Level within the ctd to use.
EnrichmentMode	[Optional] Either 'Linear' or 'Top 10%' (Default: 'Linear').
genesOutCOND	[Optional] If the analysis controlled for another GWAS, then this is included as a column. Otherwise the column is NA.
analysis_name	Used in file names which area created.
ControlForCT	[Optional] May be an internal argument. We suggest ignoring or take a look at the code to figure it out.
keep_all_rows	Keep all rows, without filtering such that there is only one row per celltype.
verbose	Print messages.

Value

Contents of the .gcov.out file.

Examples

path <- system.file(
    "extdata","ieu-a-298.tsv.gz.35UP.10DOWN.level1.MainRun.gsa.out",
    package = "MAGMA.Celltyping")
ctd <- ewceData::ctd()
annotLevel <- 1
EnrichmentMode <- "Linear"
res <- load_magma_results_file(path = path, 
                               ctd = ctd,
                               annotLevel = annotLevel,
                               EnrichmentMode = EnrichmentMode)

NathanSkene/MAGMA_Celltyping documentation built on March 5, 2025, 5:44 a.m.