Here we provide documentation on how to retrieve pre-processed dataset
from our CaDrA’s web portal. All successful responses are returned in
JSON. Only queries that respond with a 200 response
code is considered successful.
Here are standard HTTP codes that you will find in the
Status element of the response body:
Status Code
Description
200 OK
Standard HTTP successful response
404 Bad Request or Source Not Found
Standard HTTP invalid request response
500 Internal Server Error
There was an unexpected error on our server. If you see this error,
please notify us about the issue on our
GitHub
page
There are four data sources that currently available from the API.
Data
Description
Return
get_feature_set
a list of pre-proccessed feature sets available on CaDrA’s web portal
data frame
get_input_score
a list of input scores associated with a particular feature set
available on CaDrA’s web portal
data frame
get_gene_expression
a gene expression set associated with a particular feature set available
on CaDrA’s web portal
data frame
download_feature_set
a bundle of RDS files for a given feature set. Users also have the
option to whether or not to include input scores and gene expression set
that associated with that feature set.
zip file
get_feature_set
/get_feature_set
Return a list of pre-proccessed feature sets available on CaDrA’s web
portal
A data frame with two columns: description and feature_set_name
Example in R
# url for local testingurl0<-"https://montilab.bu.edu/CaDrA_API/get_feature_set"# Send GET Request to APIres<-GET(url =url0, encode ="json")# Check the status of GET request test_request<-tryCatch({stop_for_status(res)"pass"}, error =function(e){"fail"})
Output
# If GET request is successful, return the resultsif(test_request=="pass"){projects<-fromJSON(fromJSON(rawToChar(res$content)))knitr::kable(head(projects))}
description
collection
feature_set_name
CCLE SCNAs and Mutations
Somatic copy number alterations and mutations from
CCLE. See ?CaDrA::CCLE_MUT_SCNA
CCLE
CCLE SCNAs and Mutations
TCGA BrCa SCNAs and Mutations
Somatic copy number alterations and mutations from BRCA
TCGA. See ?CaDrA::BRCA_GISTIC_MUT_SIG
TCGA
TCGA BrCa SCNAs and Mutations
Simulated Feature Set
Simulated feature set comprises of 1000 genomic
features and 100 sample profiles. This simulated data includes 10
left-skewed (i.e. True Positive or TP) and 990 uniformly-distributed
(i.e. True Null or TN) features. See ?CaDrA::BRCA_GISTIC_MUT_SIG
Simulated
Simulated Feature Set
…4
ACC
TCGA
TCGA_ACC_2016_01_28_GISTIC_MUT_SIG
…5
BLCA
TCGA
TCGA_BLCA_2016_01_28_GISTIC_MUT_SIG
…6
BRCA
TCGA
TCGA_BRCA_2016_01_28_GISTIC_MUT_SIG
get_input_score
/get_input_score
Return a list of input scores associated with a given feature set
available on CaDrA’s web portal
A data frame with two columns: feature_set_name and input_score_name
Example in R
# url for local testingurl1<-"https://montilab.bu.edu/CaDrA_API/get_input_score?feature_set=TCGA_ACC_2016_01_28_GISTIC_MUT_SIG"# Send GET Request to APIres<-GET(url =url1, encode ="json")# Check the status of GET request test_request<-tryCatch({stop_for_status(res)"pass"}, error =function(e){"fail"})
Output
# If GET request is successful, return the resultsif(test_request=="pass"){projects<-fromJSON(fromJSON(rawToChar(res$content)))knitr::kable(head(projects))}
A data frame with two columns: feature_set_name and gene_expression_name
Example in R
# url for local testingurl3<-"https://montilab.bu.edu/CaDrA_API/get_gene_expression?feature_set=TCGA_ACC_2016_01_28_GISTIC_MUT_SIG"# Send GET Request to APIres<-GET(url =url3, encode ="json")# Check the status of GET request test_request<-tryCatch({stop_for_status(res)"pass"}, error =function(e){"fail"})
Output
# If GET request is successful, return the resultsif(test_request=="pass"){projects<-fromJSON(fromJSON(rawToChar(res$content)))knitr::kable(head(projects))}
feature_set_name
gene_expression_name
…1
TCGA_ACC_2016_01_28_GISTIC_MUT_SIG
TCGA_ACC_2016_01_28_Gene_Expression
download_feature_set
/download_feature_set
Return a zip file with a bundle of RDS files for a given feature set.
Users also have the option to whether or not to include input scores and
gene expression set that associated with that feature set.
whether to include gene expresion set. Default is TRUE.
string
Return
A zip file
Example in R
# url for local testingurl4<-"https://montilab.bu.edu/CaDrA_API/download_feature_set?feature_set=TCGA_ACC_2016_01_28_GISTIC_MUT_SIG&include_input_score=TRUE&inclue_gene_expression=TRUE"