Version: 2020-03-20
Usage: Rscript postgwas-exe.r <Function calls>
--base <base file(s)> --out <out folder> <options> --debug <default:FALSE>
Function calls:
--gwas A function for GWAS Catalog data.
--ldlink A function for LDlink data.
--dbdown A function for downloading databases.
--dbfilt A function for filtering data.
--dbvenn A function for venn analysis.
--dbgene A function for gene analysis.
Global arguments:
--base <Base input file path>
This is mendatory.
--out <Out folder path>
This is mendatory.
--debug <default: FALSE>
TRUE/FALSE: Rich description for debugging.
This is optional.
Running functions with "--help" argument prints [Function] usage information.gwas_catalog, v2020-01-06
This is a function for GWAS Catalog data.
Usage: Rscript postgwas-exe.r --gwas <functions> --base <base file> --out <out folder> <...>
Functions:
trait Generating pivot table for traits
gene Generating pivot table for genes
study Generating summary table for studies
filt Filtering SNPs by P-values
Global arguments:
--base <EFO0001359.tsv>
One base TSV file is mendatory.
--out <Default:data folder>
Out files target path is mendatory. Default is "data" folder.
Required arguments:
--p.criteria 5e-8
An argument for "--pivot filt". Default is 5e-8.gwas_ldlink, v2020-03-14
This is a function for LDlink data.
Usage: Rscript postgwas-exe.r --ldlink <Function> --base <base file> --out <out folder> <...>
--ldlink <Functions: dn/fl>
Functions:
down This is a function for LDlink data download.
filter This is a function for LDlink data filter.
bed This is a function for generating two BED files (hg19 and hg38).
Global arguments:
--base <EFO0001359.tsv>
One base TSV file is mendatory.
--out <default: data>
Out folder path is mendatory. Default is "data" folder.
Required arguments:
--popul <CEU TSI FIN GBR IBS ...>
An argument for the "--ldlink dn". One or more population option have to be included.
--r2d <1/2/3/4>
An argument for the "--ldlink fl". Choose one number among these options:
1) r2 >0.6 and Dprime =1 <- The most stringent criteria.
2) r2 >0.6 <- Usual choice to define LD association.
3) Dprime =1
4) r2 >0.6 or Dprime =1
5) r2 >0.8db_download, v2020-02-27
This is a function call for downloading databases
Roadmap, ENCODE, RegulomeDB, GTEx v8, and lncRNASNP2
Usage: Rscript postgwas-exe.r --dbdown <function> --out <out folder>
Functions:
roadmap Downloading Roadmap data (hg19).
encode Downloading ENCODE data (hg19).
regulome Downloading RegulomeDB data (≥2b).
gtex Downloading GTEx v8 data.
lncrna Downloading lncRNASNP2 data.
genes Downloading Ensembl Biomart Gene coordinates (hg19/hg38).
Global arguments:
--out <out folder>
Download folder path is mendatory. Default is "db" folder.
Required arguments:
--hg <hg19/hg38>
A required argument for the "genes" function. Choose one human genome version.db_filter, v2020-03-10
This is a function call for filtering data.
Usage: Rscript postgwas-exe.r --dbfilt <function> --base <base file(s)> --out <out folder> <...>
Functions:
ucsc Compile the ucsc downloaded promoter/gene/cds region annotations.
roadmap Filtering Roadmap data by enhancer tags.
gtex Filtering GTEx data by eQTL p-value.
gtex_ovl Overlapping the GTEx data with the input GWAS SNPs.
hic_bed Converting the hiC data to the BED format.
dist Filtering distance data from Bedtools closest function.
regulome Filtering and overlapping by Regulome score ≥2b.
lnc_ovl Overlapping the lncRNASNP2 data with the input GWAS SNPs.
Global arguments:
--base <base file/folder>
Base file/folder path is mendatory.
For ucsc function, you have to input three UCSC downloaded BED files by this order:
[1] cds region file, [2] whole gene region file, [3] proximal promoter region file
--out <out folder>
Out folder path is mendatory. Default is "db" folder.
Required arguments:
--ctype <cell type id>
An optional argument for the "roadmap" function.
See cell-type number information at
https://github.com/mdozmorov/genomerunner_web/wiki/Roadmap-cell-types.
--enh <default: TRUE>
An optional argument for the "roadmap" function to filter enhancer regions.
--sep <default: FALSE>
An optional argument for the "roadmap" function to generate cell-type seperated results.
--meta <roadmap meta file path>
An optional argument for the "roadmap", "dist" function.
For "roadmap" function, this argument needs "--sep TRUE" argument.
Output file will be organized by the cell types.
--infotype <default: FALSE>
An optional argument for the "dist" function.
If input as "ucsc", three output files will be generated.
[1] cds region, [2] whole gene region, [3] proximal promoter region
If input as "tags", This option allows to generate seperated output files by the tags.
--pval <p-value threshold>
A required argument for the "gtex" function to filter significant eQTLs.
--gtex <Filtered GTEx RDS file path>
A required argument for the "gtex_ovl" function to overlap GWAS SNPs with GTEx data.
--tissue <GTEx tissue name>
An optional argument for the "gtex_ovl" function to filter a specific tissue.
--regulm <Regulome data folder>
A required argument for the "regulome" function to load the data.
--lncrna <lncRNASNP2 data folder>db_venn, v2020-03-13
This is a function call for venn analysis of filtered DB data.
Usage: Rscript postgwas-exe.r --dbvenn <function> --base <base files> --out <out folder> --fig <figure out folder>
Functions:
venn Venn analysis of rsids.
summ Generating summary table with annotations.
Global arguments:
--base <base files>
At least 2 Base BED file paths are mendatory.
For the venn function,if the base file number is over 4, then venn diagram is not generated.
--out <out folder>
Out folder path is mendatory. Default is "data" folder.
Required arguments:
--fig <figure out folder>
An optional argument for the "venn" function to save figure file.
If no figure out path is designated, no venn figure will generated.
--uni_list <default: FALSE>
An optional argument for the "venn" function.
To return the union SNP list.
--sub_dir <default: FALSE>
An optional argument for the "summ" function.
To get file paths grouped by the subfoler.
--uni_save <default: TRUE>
An optional argument for the "summ" function.
To save to union SNP list as a BED file.
--ann_gwas <GWAS annotation TSV file>
An optional argument for the "summ" function.
Add GWAS annotations to the summary table 1.
--ann_encd <ENCODE annotation dist file>
An optional argument for the "summ" function.
Add ENCODE annotations to the summary table 2.
--ann_near <Nearest gene annotation dist file>
An optional argument for the "summ" function.
Add nearest gene annotations to the summary table 3.
--ann_cds <Gene CDS annotation dist file>
An optional argument for the "summ" function.
Add gene CDS annotations to the summary table 3.
--ann_gtex <GTEx eQTL annotation TSV file>
An optional argument for the "summ" function.
Add GTEx eQTL annotations to the summary table 4.
--ann_lnc <lncRNA annotation TSV file>
An optional argument for the "summ" function.
Add lncRNA annotations to the summary table 5.
Version: v2020-03-25
This is a function call for gene analysis to compile the Hi-C and eQTL data.
Usage: Rscript postgwas-exe.r --dbgene <function> --base <base files> --out <out folder>
Functions:
hic_pair Extract Hi-C linked SNP-Gene pairs.
gtex_pair Extract eQTL linked SNP-Gene pairs.
summary Summarizing GWAS SNPs-Gene pairs.
david_go Summarizing DAVID GO analysis result.
Global arguments:
--base <base files>
For "hic_pair" function, two input files are:
[1] gwas_dist file, [2] gene_dist file
--out <out folder>
Out folder path is mendatory. Default is "data" folder.
Required arguments:
--bed <default:FALSE>
An optional argument for the "hic_pair" function.
To save as BED format file.
--nearest <nearest gene summary file path>
An optional argument for the "summary" function.
Add nearest gene summary table to the hic gene summary.
--fdr <default:0.05>
An optional argument for the "david_go" function.