runGIGSEA {GIGSEA} | R Documentation

## runGIGSEA

### Description

runGIGSEA use MetaXcan to impute the trait-associated differential gene expression from GWAS summary and eQTL database first, and next, performs gene set enrichment analysis for the trait-associated SNPs.

### Usage

    runGIGSEA(MetaXcan, model_db_path, covariance, gwas_folder, gwas_file_pattern,
      snp_column = "SNP", non_effect_allele_column = "A2",
      effect_allele_column = "A1", or_column = "OR", beta_column = "BETA",
      beta_sign_column = "direction", zscore_column = "Z",
      pvalue_column = "P", gene_set = c("MSigDB.KEGG.Pathway", "MSigDB.TF",
      "MSigDB.miRNA", "TargetScan.miRNA"), permutation_num = 1000,
      output_dir = "./GIGSEA", MGSEA_thres = NULL, verbose = TRUE)

### Arguments

`MetaXcan` | a character value indicating the path to the MetaXcan.py file.
`model_db_path` | a character value indicating the path to tissue transriptome model.
`covariance` | a character value indicating the path to file containing covariance information. This covariance should have information related to the tissue transcriptome model.
`gwas_folder` | a character value indicating the folder containing GWAS summary statistics data.
`gwas_file_pattern` | a regular expression indicating the gwas summary files.
`snp_column` | a character value indicating the name of column holding SNP data, by default, "SNP".
`non_effect_allele_column` | a character value indicating the name of column holding "other/non effect" allele data, by default, "A2".
`effect_allele_column` | a character value indicating the name of column holding effect allele data, by default, "A1".
`or_column` | a character value indicating the name of column holding Odd Ratio data, by default, "OR".
`beta_column` | a character value indicating the name of column holding beta data, by default, "BETA".
`beta_sign_column` | a character value indicating the name of column holding sign of beta, by default, "direction".
`zscore_column` | a character value indicating the name of column holding zscore of beta, by default, "Z".
`pvalue_column` | a character value indicating the name of column holding p-values data, by default, "P".
`gene_set` | a vector of characters indicating the gene sets of interest for enrichment test, by default, c("MSigDB.KEGG.Pathway","MSigDB.TF", "MSigDB.miRNA","Fantom5.TF","TargetScan.miRNA","GO", "LINCS.CMap.drug")
`permutation_num` | an integer indicating the number of permutation.
`output_dir` | a character value indicating the directory for saving the results.
`MGSEA_thres` | an integer value indicating the thresfold for performing MGSEA. When the number of gene sets is smaller than MGSEAthres, we perform MGSEA.
`verbose` | an boolean value indicating whether or not to print output to the screen

### Value

TRUE

### Author(s)

Shijia Zhu, shijia.zhu@mssm.edu

### References

Barbeira, A., et al. Integrating tissue specific mechanisms into GWAS summary results. bioRxiv 2016:045260. https://github.com/hakyimlab/MetaXcan

### See Also

`weightedGSEA`;

### Examples

    # runGIGSEA( MetaXcan="/MetaXcan/software/MetaXcan.py" ,
      # model_db_path="data/DGN-WB_0.5.db" ,
      # covariance="data/covariance.DGN-WB_0.5.txt.gz" ,
      # gwas_folder="data/GWAS" ,
      # gwas_file_pattern="heart.summary" ,
      # zscore_column="Z" ,
      # output_dir="./GIGSEA",
      # permutation_num=1000)

[Package GIGSEA version 1.0.0 Index]