tests/testthat/test_gwascat.R

In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

#tt38saved.old = structure(c(957L, 699L, 649L, 323L, 294L, 249L, 248L, 245L, 222L, 
#197L), .Dim = 10L, .Dimnames = structure(list(c("Obesity-related traits", 
#"IgG glycosylation", "Height", "Type 2 diabetes", "Rheumatoid arthritis", 
#"Crohn's disease", "Schizophrenia", "Blood metabolite levels", 
#"HDL cholesterol", "Breast cancer")), .Names = ""))
#
## as of 18 Jan 2016
#
#tt38saved = structure(c(957L, 822L, 699L, 340L, 294L, 249L, 248L, 245L, 222L, 
#199L), .Dim = 10L, .Dimnames = structure(list(c("Obesity-related traits", 
#"Height", "IgG glycosylation", "Type 2 diabetes", "Rheumatoid arthritis", 
#"Crohn's disease", "Schizophrenia", "Blood metabolite levels", 
#"HDL cholesterol", "Breast cancer")), .Names = ""), class = "table")
#
#library(gwascat)
#checkTrue(identical(topTraits(ebicat38), as.table(tt38saved)))
#
#colnames_2016jan18 = c("DATE ADDED TO CATALOG", "PUBMEDID", "FIRST AUTHOR", "DATE", 
#"JOURNAL", "LINK", "STUDY", "DISEASE/TRAIT", "INITIAL SAMPLE DESCRIPTION", 
#"REPLICATION SAMPLE DESCRIPTION", "REGION", "CHR_ID", "CHR_POS", 
#"REPORTED GENE(S)", "MAPPED_GENE", "UPSTREAM_GENE_ID", "DOWNSTREAM_GENE_ID", 
#"SNP_GENE_IDS", "UPSTREAM_GENE_DISTANCE", "DOWNSTREAM_GENE_DISTANCE", 
#"STRONGEST SNP-RISK ALLELE", "SNPS", "MERGED", "SNP_ID_CURRENT", 
#"CONTEXT", "INTERGENIC", "RISK ALLELE FREQUENCY", "P-VALUE", 
#"PVALUE_MLOG", "P-VALUE (TEXT)", "OR or BETA", "95% CI (TEXT)", 
#"PLATFORM [SNPS PASSING QC]", "CNV", "MAPPED_TRAIT", "MAPPED_TRAIT_URI"
#)
#
#colnames_2016apr03 = c("DATE ADDED TO CATALOG", "PUBMEDID", "FIRST AUTHOR", "DATE", 
#"JOURNAL", "LINK", "STUDY", "DISEASE/TRAIT", "INITIAL SAMPLE DESCRIPTION", 
#"REPLICATION SAMPLE DESCRIPTION", "REGION", "CHR_ID", "CHR_POS", 
#"REPORTED GENE(S)", "ENTREZ_MAPPED_GENE", "ENSEMBL_MAPPED_GENE", 
#"ENTREZ_UPSTREAM_GENE_ID", "ENTREZ_DOWNSTREAM_GENE_ID", "ENSEMBL_UPSTREAM_GENE_ID", 
#"ENSEMBL_DOWNSTREAM_GENE_ID", "SNP_GENE_IDS_ENTREZ", "SNP_GENE_IDS_ENSEMBL", 
#"ENTREZ_UPSTREAM_GENE_DISTANCE", "ENTREZ_DOWNSTREAM_GENE_DISTANCE", 
#"ENSEMBL_UPSTREAM_GENE_DISTANCE", "ENSEMBL_DOWNSTREAM_GENE_DISTANCE", 
#"STRONGEST SNP-RISK ALLELE", "SNPS", "MERGED", "SNP_ID_CURRENT", 
#"CONTEXT", "INTERGENIC_ENTREZ", "INTERGENIC_ENSEMBL", "RISK ALLELE FREQUENCY", 
#"P-VALUE", "PVALUE_MLOG", "P-VALUE (TEXT)", "OR or BETA", "95% CI (TEXT)", 
#"PLATFORM [SNPS PASSING QC]", "CNV", "MAPPED_TRAIT", "MAPPED_TRAIT_URI"
#)
#