diff --git a/DESCRIPTION b/DESCRIPTION index bacd25f1178b20e3cd8217d7ff6b26e9daffff58..4decac6c2673e72c7f13a9c99ece79b362cfc610 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: ViSEAGO -Version: 1.3.14 +Version: 1.3.15 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity Author: Aurelien Brionne [aut, cre], Amelie Juanchich [aut], diff --git a/R/merge_enrich_terms.R b/R/merge_enrich_terms.R index 935003a89774b0b6fb84a2c0d4ead09fe2e13be0..ac8d79af6a7ac3f66f681c6d91fe5ef060461165 100644 --- a/R/merge_enrich_terms.R +++ b/R/merge_enrich_terms.R @@ -545,6 +545,54 @@ setMethod( } } + # if db match to Custom + if(db[1]=="Uniprot-GOA"){ + + # temp file + temp<-paste( + tempfile(), + "gz", + sep="." + ) + + # load the file + download.file( + paste( + 'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/', + toupper(db[2]), + '/goa_', + db[2], + '.gaf.gz', + sep="" + ), + destfile =temp, + quiet=TRUE, + method="internal" + ) + + # unzip + gunzip(temp) + + # read file + annot<-unique( + fread( + sub("\\.gz","",temp), + skip=12, + select=c(2,3), + col.names=c("gene_id","gene_symbol") + ) + ) + + # merge gene_symbol + genes<-merge( + genes, + annot, + by.x="Significant_genes", + by.y="gene_id", + all.x=TRUE + ) + } + # if db match to Custom if(db[1]=="Custom"){ diff --git a/README.md b/README.md index 9caeb366399a9499d817fa0bc25a8f56792126c0..92311f652e2b72df114140370ac89eeb56a087f7 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ remotes::install_gitlab( devtools::build("ViSEAGO") # install package (from R console) - install.packages("ViSEAGO_1.3.14.tar.gz", repos = NULL, type = "source") + install.packages("ViSEAGO_1.3.15.tar.gz", repos = NULL, type = "source") ``` ## Citation