From e97c74b39c535a4e8706323d5ff49fc57a7a8174 Mon Sep 17 00:00:00 2001 From: John Elizarraras Date: Thu, 10 Aug 2023 16:51:32 -0500 Subject: [PATCH] add function documentation --- README.Rmd | 9 +++++++++ README.md | 16 ++++++++++++++++ 2 files changed, 25 insertions(+) diff --git a/README.Rmd b/README.Rmd index 8b6b1b6..565edad 100644 --- a/README.Rmd +++ b/README.Rmd @@ -29,6 +29,15 @@ You can install the development version of clinicalomicsdbR from [GitHub](https: devtools::install_github("bzhanglab/clinicalomicsdbR") ``` +## 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. + +See the examples below for more information on how to use. + ## Examples ### Filter and Download diff --git a/README.md b/README.md index 1d5ed0b..e5dff3d 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,22 @@ You can install the development version of clinicalomicsdbR from devtools::install_github("bzhanglab/clinicalomicsdbR") ``` +## 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 + list, with column `study_list` that contains the names of the + studies and `df` that contains a list of the study data information. + +See the examples below for more information on how to use. + ## Examples ### Filter and Download