diff --git a/README.Rmd b/README.Rmd index 565edad..7383964 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,7 +18,9 @@ knitr::opts_chunk$set( -R package to interface with the ClinicalOmicsDB API. Designed with the structure from https://r-pkgs.org/. +R package to interface with the ClinicalOmicsDB API. Can be used to download data for your own analysis, or directly load study information into a dataframe for exploration. + +Designed with the structure from https://r-pkgs.org/. ## Installation @@ -29,12 +31,28 @@ You can install the development version of clinicalomicsdbR from [GitHub](https: devtools::install_github("bzhanglab/clinicalomicsdbR") ``` +See Examples below to see how to use. + +## Parameters + +- `hostname` - base URL of the website containing the ClinicalOmicsDB API. Only change if you are running a custom service. +- `study_list` - list containing all the studies that were filtered by the `filter()` function. + ## Functions -- `new()` - Create new clinicalomicsdbR object. Needed before any other function -- `filter(drugs, cancers)` - filters studies matching provided arugments. `drugs` is a list and can be individual drugs or combinations. See the ClinicalOmicsDB website for all options. `cancers` can contain multiple cancers. -- `download(output_dir)` - downloads all studies from `filter()` into `output_dir`. `output_dir` is optional, and defaults to `clindb` -- `dataframe()` - loads all the studies from `filter()` into a dataframe, with column `study_list` that contains the names of the studies and `df` that contains a list of the study data information. +- `new()` - Create new clinicalomicsdbR object. Needed before any other + function +- `filter(drugs, cancers)` - filters studies matching provided + arugments. `drugs` is a list and can be individual drugs or + combinations. See the ClinicalOmicsDB website for all options. + `cancers` can contain multiple cancers. +- `download(output_dir)` - downloads all studies from `filter()` into + `output_dir`. `output_dir` is optional, and defaults to `clindb` +- `dataframe()` - loads all the studies from `filter()` into a + list, with column `study_list` that contains the names of the + studies and `df` that contains a list of the study data information. +- `dataframe_from_id(study_id)` - loads a study with id from `study_id` into a dataframe +- `downlaod_from_id(study_id, output_dir)` - downsloads a study with id from `study_id` into a folder `output_dir`. `output_dir` defaults to `clindb` See the examples below for more information on how to use. diff --git a/README.md b/README.md index e5dff3d..5f469b6 100644 --- a/README.md +++ b/README.md @@ -6,8 +6,9 @@ -R package to interface with the ClinicalOmicsDB API. Designed with the -structure from . +R package to interface with the ClinicalOmicsDB API. Can be used to download data for your own analysis, or directly load study information into a dataframe for exploration. + +Designed with the structure from https://r-pkgs.org/. ## Installation @@ -19,6 +20,15 @@ You can install the development version of clinicalomicsdbR from devtools::install_github("bzhanglab/clinicalomicsdbR") ``` +See Examples below to see how to use. + +## Parameters + +- `hostname` - base URL of the website containing the ClinicalOmicsDB + API. Only change if you are running a custom service. +- `study_list` - list containing all the studies that were filtered by + the `filter()` function. + ## Functions - `new()` - Create new clinicalomicsdbR object. Needed before any other @@ -29,9 +39,14 @@ devtools::install_github("bzhanglab/clinicalomicsdbR") `cancers` can contain multiple cancers. - `download(output_dir)` - downloads all studies from `filter()` into `output_dir`. `output_dir` is optional, and defaults to `clindb` -- `dataframe()` - loads all the studies from `filter()` into a - list, with column `study_list` that contains the names of the - studies and `df` that contains a list of the study data information. +- `dataframe()` - loads all the studies from `filter()` into a list, + with column `study_list` that contains the names of the studies and + `df` that contains a list of the study data information. +- `dataframe_from_id(study_id)` - loads a study with id from `study_id` + into a dataframe +- `downlaod_from_id(study_id, output_dir)` - downsloads a study with id + from `study_id` into a folder `output_dir`. `output_dir` defaults to + `clindb` See the examples below for more information on how to use.