## ---- echo=FALSE, message=FALSE------------------------------------------
library(CollateralVulnerability2016)
library(dplyr)
## ----eval=FALSE----------------------------------------------------------
# work_dir <- '~/BigData/CollateralVulnerability2016/demo/'
# download_dir <- '~/BigData/RTCGA_downloads/'
# mydb <- 'demo_output.db'
# mydb_path <- paste0(work_dir, mydb)
# my_con <- setupSQLite ( mydb_path )
#
## ----eval=FALSE----------------------------------------------------------
# all_genes <- getAllHumanGenes(my_con)
# head(all_genes)
#
## ----eval=FALSE----------------------------------------------------------
# src_sqlite(my_con@dbname) %>% tbl('human_genes')
## ----eval=FALSE----------------------------------------------------------
#
# rnaseq_dat <- getTCGARNAseqData(my_con, cancerTypes='LUAD', releaseDate = '2015-11-01', sampletag=c('01A', '06A'))
# dim(rnaseq_dat)
#
# mutation_dat <- getTCGAMutationData(my_con, cancerTypes='LUAD', releaseDate = '2015-11-01', sampletag=c('01A', '06A'))
# dim(mutation_dat)
#
# DBI::dbListTables(my_con)
#
## ----eval=FALSE----------------------------------------------------------
#
# bisep_output <- doBISEPAnalysis(my_con, genes_n=100000)
# #bisep_output <- doBISEPAnalysis(my_con, genes_n=1000)
#
## ----eval=FALSE----------------------------------------------------------
#
# bisep_results <- src_sqlite(my_con@dbname) %>%
# dplyr::tbl('bisep_results') %>%
# dplyr::filter(bisep_pval < 0.1 & pi_value <0.2) %>%
# dplyr::collect() %>%
# # dplyr::slice(1:100) %>%
# inner_join(all_genes, by=c('gene_name'='gene_id')) %>%
# dplyr::select(gene_name, gene_name.y, everything()) %>%
# dplyr::arrange(gene_name.y)
# bisep_results
#
## ----eval=FALSE----------------------------------------------------------
# doRNAseqPlot(my_con, 'ENSG00000176024')
#
## ----eval = FALSE--------------------------------------------------------
#
# human_paralog_res <- countHumanParalogs(my_con, bisep_results$gene_name)
# #human_paralog_res <- countHumanParalogs(my_con, sample(all_genes$gene_id, 1000))
#
## ----eval = FALSE--------------------------------------------------------
#
# fly_orthologs <- getOrthologs(my_con, results$gene_name, 'dmelanogaster')
# flymine_res <- doFlyMineAnalysis(my_con, bisep_results$gene_name)
# #flymine_res <- doFlyMineAnalysis(my_con, sample(all_genes$gene_id, 1000))
#
## ----eval = FALSE--------------------------------------------------------
#
# worm_orthologs <- getOrthologs(my_con, results$gene_name, 'celegans')
# wormmine_res <- doWormMineAnalysis(my_con, bisep_results$gene_name)
# #wormmine_res <- doWormMineAnalysis(my_con, sample(all_genes$gene_id, 1000))
#
## ----eval = FALSE--------------------------------------------------------
#
# mut_res <- doMutationAnalysis(my_con, bisep_results$gene_name)
# #mut_res <- doMutationAnalysis(my_con, sample(all_genes$gene_id, 1000))
#
## ----eval=FALSE----------------------------------------------------------
# combo_res <- combineResults(my_con, bisep_results$gene_name)
## ----eval=FALSE----------------------------------------------------------
# filtered_results <- src_sqlite(my_con@dbname) %>%
# dplyr::tbl('combined_results') %>%
# dplyr::filter(count_paralogs > 0 & count_paralogs <= 5 & (lethal_pct_fly >= 20 | lethal_pct_worm >= 20) ) %>%
# dplyr::collect()
## ----eval=FALSE----------------------------------------------------------
# shinyVisApp(my_con)
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