Description Usage Arguments Value
View source: R/LDSC_Pipeline_Functions.R
#' 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/
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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. |
Will run heritability script for all annotations and GWASs.
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