Using clinicaltrials.gov database in R - r

Question

I am trying to use R to access the clinicaltrials.gov AACT database to create a list of facility_investigators for a specific topic.
The following code is an example of how to get a list of all clinical trials on the topic TP53
library(dplyr)
library(RPostgreSQL)
aact = src_postgres(dbname = 'aact',
host = "aact-db.ctti-clinicaltrials.org",
user = 'aact',
password = 'aact')
study_tbl = tbl(src=aact, 'studies')
x = study_tbl %>% filter(official_title %like% '%TP53%') %>% collect()
Similarly, if I want a list of principal investigators,
library(dplyr)
library(RPostgreSQL)
aact = src_postgres(dbname = 'aact',
host = "aact-db.ctti-clinicaltrials.org",
user = 'aact',
password = 'aact')
study_tbl = tbl(src=aact, 'facility_investigators')
I am unable to make a list on only TP53 facility_investigators. Something like TP53 & facility_investigators. Any help would be appreciated
This is a link where some explanation is provided, but my problem is not resolved - http://www.cancerdatasci.org/post/2017/03/approaches-to-accessing-clinicaltrials.gov-data/

Answer 1

Is this what your asking...Your pulling from two different tables in the same database the first one is 'studies' and the second one is 'facilities investigators'. What you need to do is run the head() command for each of the tables (or run glimpse() or run str()) and see if the two tables have a common variable you can merge on after you load them into R. If they do then you would do something like this:
library(dplyr)
merged_table <- inner_join(x, study_table, by = "common column")
If the columns have different names it would like:
library(dplyr)
merged_table <- inner_join(x, study_table, by = c("x_column_name" = "study_table_column_name"))
From there you can limit your dataset to just facility investigators that have the characteristics you want.
If you want to do it in one PostgreSQL query you can do it like so. For more information about this syntax in particular see page 18:
con <- dbConnect() # use the same parameters you use above to connect
query <- dbSendQuery(con,
'select s.*, fi.*
from (select * from studies where official_title like "%TP53%")
as s
inner join facility_investigators as fi
on s."joining column" = fi."joining column"'
)
r_dataset <- fetch(query)
# I would just close the connection in RStudio using the connection tab.
The above query has an inner join in the main query and a subquery in the from statement. The subquery performs the filtering you where trying to do in R. It essentially allows you to select only from the table where the results are already filtered. An inner join combines all the records the two tables have in common and puts them into one table. If you need to join on more than one column add an 'and' between the two statements in the on statement.