runGIGSEA: runGIGSEA
In zhushijia/GIGSEA: Genotype Imputed Gene Set Enrichment Analysis

Description Usage Arguments Value Author(s) References See Also Examples

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.

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)

`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","TargetScan.miRNA")
`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

TRUE

Shijia Zhu, shijia.zhu@mssm.edu

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

weightedGSEA;

# 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)