Error in getParalogs

[komalsrathi]

I am facing another issue with few genes in getParalogs function:

Code:

library(drugTargetInteractions)
genes <- c("FGFBP2", "HOXC6", "FREM2", "HOXC9", "AC105052.1")
chembldb <- system.file("extdata", "chembl_sample.db", package="drugTargetInteractions")
resultsPath <- system.file("extdata", "results", package="drugTargetInteractions")
config <- genConfig(chemblDbPath=chembldb, resultsPath=resultsPath)
downloadUniChem(config=config)
cmpIdMapping(config=config)

# convert to ensembl gene id - gene symbol vector
idMap <- getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids = genes, idtype = "GENE_NAME")
ens_gene_id <- idMap$ens_gene_id
queryBy <- list(molType="gene", idType = "ensembl_gene_id", ids = names(ens_gene_id))
res_list <- getParalogs(queryBy)

Error:

Error in rep(seq_along(resultDF$ENSEMBL), index) : 
  invalid 'times' argument

[tgirke]

I believe you have the same problem as in your previous comment, as you are using the path from system.file()?

[komalsrathi]

I downloaded the full database and still getting the same error:

library(drugTargetInteractions)
genes <- c("FGFBP2", "HOXC6", "FREM2", "HOXC9", "AC105052.1")

# obtained from ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/chembl_29_sqlite.tar.gz
chembldb <- file.path(ref_dir, "chembl", "chembl_29_sqlite", "chembl_29.db")
resultsPath <- system.file("extdata", "results", package = "drugTargetInteractions")
config <- genConfig(chemblDbPath = chembldb, resultsPath = resultsPath)
downloadUniChem(config = config)
cmpIdMapping(config = config)

idMap <- getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids = genes, idtype = "GENE_NAME")
ens_gene_id <- idMap$ens_gene_id
queryBy <- list(molType="gene", idType = "ensembl_gene_id", ids = names(ens_gene_id))
res_list <- getParalogs(queryBy)

Error in rep(seq_along(resultDF$ENSEMBL), index) : 
  invalid 'times' argument

[tgirke]

This works for me. Perhaps first install the updated package as instructed in your other issue. Also pay attention to the other line with system.file. Just in case this is the code I tested with your gene ids:

1. Load package and enrionment settings

Same as in other issue...

2. Query with gene symbols for paralogs

gene_name <- c("FGFBP2", "HOXC6", "FREM2", "HOXC9", "AC105052.1")                                                                                                                                                                                                          
idMap <- getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids = gene_name, idtype = "GENE_NAME")                                                                                                                                                                                  
ens_gene_id <- idMap$ens_gene_id                                                                                                                                                                                                                                           
queryBy <- list(molType="gene", idType = "ensembl_gene_id", ids = names(ens_gene_id))                                                                                                                                                                                      
res_list <- getParalogs(queryBy)  

[komalsrathi]

Works as expected, thanks!