S-LDSC scripts for use on MR server. This will only run on the MR server, as some of the arguments are hard-coded directory paths. If user wishes to use the package locally, clone the package into your own server and change the appropriate arguments listed in get_LDSC_fixed_args
and Create_GWAS_df
functions found in LDSC_Pipeline_Functions.R, as well as the creating_baseline_df
function found in LDSC_Creatingannot_Functions.R.
Scripts make use of the command line tool ldsc
. For more information on S-LDSC, please refer to:
- https://github.com/bulik/ldsc/wiki
- https://www.ncbi.nlm.nih.gov/pubmed/26414678
To use, install from github. This can be done using the following lines of code:
install.packages("devtools")
library(devtools)
install_github("RHReynolds/LDSCforRyten")
Running S-LDSC can be divided into the following steps. 1. Creating an .annot file. This is a file consisting of CHR, BP, SNP, and CM columns, followed by a column for your annotation, with the value of the annotation for each SNP (0/1 for binary annotations or arbitrary numbers for continuous annotations). It is important that SNPs are provided in the same order as the .bim file used for the computation LD scores. To ensure this is the case, the easiest thing to do is to find those SNPs from an annotation (which may be genes, or genomic regions) that overlap with the baseline model that is used for computation of LD scores. 2. Computing LD scores for the annotation. 3. Partitioning heritability by annotation, using the baseline model. 4. Collating and summarising the output of S-LDSC.
For an example of this process run from end to end, please refer to this tutorial.
Script | Description | Author(s)
------ | ----------- | ---------
GWAS_formatting_functions.R | Functions that can be used to format and liftover GWAS from hg19/GRCh37 to GRCh38. | RHR
LDSC_Creatingannot_Functions.R | Functions that can be used for creating binary .annot.gz files prior to running LDSC_Pipeline_Functions.R. | RHR
LDSC_Pipeline_Entire.R | Pipeline for running stratified LDSC with a binary annotation and it's subcategories. This requires that the user has created the appropriate .annot.gz files. Note that this pipeline is divided into two steps: 1) calculating LD scores for an annotation and 2) partitioning heritability in the annotation. If necessary, these two steps can be run separately. Call the script using: Rscript /path/to/script/LDSC_Pipeline_Functions.R -h
. The -h
flag will list the required inputs and optional arguments. | RHR
LDSC_SummariseOutput_Functions.R | Functions that can be used to summarise the output of S-LDSC once pipeline has been run. | RHR
/data/LDScore/Reference_Files/
. They are also available via the Alkes lab repository, and descriptions of necessary reference files can be found described in the ldsc
wiki page./data/LDScore/GWAS/
ldsc
wiki page for details on how to prepare GWAS summary statistics for use with ldsc
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