Calculate_H2: Function to run LDSC heritability script for a number of...

In RHReynolds/LDSCforRyten: Run LDSC on Ryten Lab Server

Description

#' Note: For this to be able to run, annot.gz files should be stored in: $ANNOTATION_BASEDIR/$ANNOT_NAME/$ANNOTATION_SUBCATEGORY/ where $ANNOTATION_BASEDIR refers to the common directory, $ANNOT_NAME refers to the author of article from which the annotation is derived and $ANNOTATION_SUBCATEGORY refers to the subcategories within the annotation. Function should be run in the folder $ANNOT_NAME/

Usage

Calculate_H2(
  Annotation_Basedir = NULL,
  Annot_name = NULL,
  Annotation_Subcategories = NULL,
  Fixed_Arguments = NULL,
  GWAS_df = NULL,
  cores = 1
)

Arguments

Annotation_Basedir	Common directory wherein specific annotation is stored.
Annot_name	Name of annotation. This should be written exactly as written in the annotation directory name.
Annotation_Subcategories	Annoation subcategories. If there is more than 1, these should be written precisely as in the folder, and should be entered with a comma separator without any spaces.
Fixed_Arguments	List of fixed arguments. This can be created using the get_LDSC_fixed_args() function.
GWAS_df	Dataframe of GWAS to be run in the H2 estimation, as generated using the Create_GWAS_df() function. Columns should include: Full.paths (full paths to GWAS), Original.name (original name of sumstat.gz file), Output.prefix (alternative output name).
cores	integer. Number of cores to parallelise across. Default = 1.

Value

Will run heritability script for all annotations and GWASs.

RHReynolds/LDSCforRyten documentation built on Sept. 27, 2021, 5:20 p.m.