## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----loading_xkr4_tables, warning=FALSE------------------------------------ # Chemicals - XKR4 bq_xkr4_c <- system.file( paste0( "extdata", .Platform$file.sep, "bq_xkr4_chem.tsv" ), package="CTDquerier" ) nrow( read.delim( bq_xkr4_c, sep = "\t" ) ) # Diseses curated - XKR4 bq_xkr4_dC <- system.file( paste0( "extdata", .Platform$file.sep, "bq_xkr4_disease_curated.tsv" ), package="CTDquerier" ) nrow( read.delim( bq_xkr4_dC, sep = "\t" ) ) # Diseases inferred - XKR4 bq_xkr4_dI <- system.file( paste0( "extdata", .Platform$file.sep, "bq_xkr4_disease_inferred.tsv" ), package="CTDquerier" ) nrow( read.delim( bq_xkr4_dI, sep = "\t" ) ) # Diseases all - XKR4 bq_xkr4_dA <- system.file( paste0( "extdata", .Platform$file.sep, "bq_xkr4_disease_all.tsv" ), package="CTDquerier" ) nrow( read.delim( bq_xkr4_dA, sep = "\t" ) ) ## ----ctdquerier_xkr4------------------------------------------------------- library( CTDquerier ) xkr4 <- query_ctd_gene( terms = "XKR4", verbose = TRUE ) xkr4 ## ----compare_xkr4_chemicals------------------------------------------------ # How many unique chemicals associations there are in the result object? xkr4_chem <- get_table( xkr4, index_name = "chemical interactions" ) length( unique( xkr4_chem$Chemical.Name ) ) # How many of the chemicals download using CTDquerier are in the Batch Query files? bq_xkr4_c <- read.delim( bq_xkr4_c, sep = "\t" ) sum( as.character( bq_xkr4_c[ , 2] ) %in% unique( xkr4_chem$Chemical.Name ) ) ## -------------------------------------------------------------------------- dim( get_table( xkr4, index_name = "diseases" ) ) ## -------------------------------------------------------------------------- bq_xkr4_dA <- read.delim( bq_xkr4_dA, sep = "\t" ) length( unique( bq_xkr4_dA$DiseaseID ) ) sum( as.character( unique( bq_xkr4_dA$DiseaseID ) ) %in% get_table( xkr4, index_name = "diseases" )$Disease.ID ) ## -------------------------------------------------------------------------- bq_xkr4_dA[1:3, ] ## -------------------------------------------------------------------------- tbl <- get_table( xkr4, index_name = "diseases" ) tbl[ tbl$Disease.ID == "MESH:D015746", "Inference.Network" ] ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()