Title: R Client Library for CloudOS
Version: 0.4.0
Description: The 'CloudOS' client library for R makes it easy to interact with CloudOS in the R environment for analysis.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.2
Imports: httr, utils, methods, dplyr (≥ 1.0.0), tidyr, jsonlite, rappdirs, ggplot2, tibble
Suggests: httptest, kableExtra, knitr, lintr, rmarkdown, testthat
URL: https://github.com/lifebit-ai/cloudos
BugReports: https://github.com/lifebit-ai/cloudos/issues
NeedsCompilation: no
Packaged: 2023-03-17 14:18:42 UTC; sksahu
Author: Sangram Keshari Sahu [aut, cre], Ilya Levantis [aut], Henry Stewart [aut], Lifebit Biotech Ltd. [cph]
Maintainer: Sangram Keshari Sahu <sangram@lifebit.ai>
Repository: CRAN
Date/Publication: 2023-03-17 14:50:02 UTC

Apply a query to a cohort

Description

Updates a cohort by applying a new query.

Usage

cb_apply_query(cohort, query, keep_query = TRUE)

Arguments

cohort

A cohort object. (Required) See constructor function cb_create_cohort or cb_load_cohort

query

A phenotype query defined using the phenotype function and logic operators (see example below)

keep_query

If True, combines the newly supplied query with the pre-existing query. Otherwise, pre-existing query is overwritten. (Default: TRUE)

Value

The updated cohort object.

Examples

## Not run: 
A <- phenotype(id = 13, from = "2016-01-21", to = "2017-02-13")
B <- phenotype(id = 4, value = "Cancer")

A_not_B <- A & !B

my_cohort <- cb_load_cohort(cohort_id = "612f37a57673ed0ddeaf1333", cb_version = "v2")

my_cohort <- cb_apply_query(my_cohort, query = A_not_B, keep_query = F)

## End(Not run)

Create Cohort

Description

Creates a new Cohort

Usage

cb_create_cohort(cohort_name, cohort_desc, filters = "", cb_version = "v2")

Arguments

cohort_name

New cohort name to be created. (Required)

cohort_desc

New cohort description to be created. (Optional)

filters

WIP - details will be added.

cb_version

cohort browser version. ["v1" | "v2"] (Optional) Default - "v2"

Value

A cohort object.

See Also

cb_load_cohort for loading a available cohort.

Examples

## Not run: 
my_cohort <- cb_create_cohort(cohort_name = "Cohort-R",
                              cohort_desc = "This cohort is for testing purpose, created from R.")

## End(Not run)

Get genotypic table

Description

Get Genotypic table in a dataframe. Optionally genotypic filters can be applied as well.

Usage

cb_get_genotypic_table(cohort, size = 10, geno_filters_query)

Arguments

cohort

A cohort object. (Required) See constructor functions cb_create_cohort or cb_load_cohort

size

Number of entries from database. (Optional) Default - 10 (Optional)

geno_filters_query

Genotypic filter query (Optional)

Value

A dataframe.

Get participant data table

Description

Get participant data table in a dataframe.

Usage

cb_get_participants_table(cohort, cols, page_number = "all", page_size = 5000)

Arguments

cohort

A cohort object. (Required) See constructor functions cb_create_cohort or cb_load_cohort

cols

Vector of phenotype IDs to fetch as columns in the dataframe. If omitted, columns saved in the cohort are fetched.

page_number

Number of page as integer or 'all' to fetch all data. (Optional) Default - 'all'

page_size

Number of entries in a page. (Optional) Default - 5000

Value

A dataframe.

Get longform participant data table

Description

Get participant data table in a longform dataframe.

Usage

cb_get_participants_table_long(
  cohort,
  cols,
  broadcast = TRUE,
  page_number = 0,
  page_size = 100
)

Arguments

cohort

A cohort object. (Required) See constructor functions cb_create_cohort or cb_load_cohort

cols

Vector of phenotype IDs to fetch as columns in the dataframe. If omitted, columns saved in the cohort are fetched.

broadcast

Whether to broadcast single value phenotypes across rows. (Optional) Can be TRUE, FALSE or a vector of phenotype IDs to specify which phenotypes to broadcast. Default - TRUE

page_number

Number of page (can be 'all' to fetch all data) . (Optional) Default - 0

page_size

Number of entries in a page. (Optional) Default - 10

Value

A tibble.

Phenotype metadata

Description

Get the metadata of a phenotype in the cohort browser

Usage

cb_get_phenotype_metadata(pheno_id, cb_version = "v2")

Arguments

pheno_id

A phenotype ID. (Required)

cb_version

cohort browser version. (Default: "v2") [ "v1" | "v2" ]

Value

A data frame.

Get distribution of a phenotype in a cohort

Description

Retrieve a data frame containing the distirbution data for a specific phenotype within a cohort.

Usage

cb_get_phenotype_statistics(
  cohort,
  pheno_id,
  max_depth = Inf,
  page_number = "all",
  page_size = 1000
)

Arguments

cohort

A cohort object. (Required) See constructor function cb_create_cohort or cb_load_cohort

pheno_id

A phenotype ID. (Required)

max_depth

The maximum depth to descend in a 'nested list' phenotype. (Default: Inf)

page_number

For internal use.

page_size

For internal use.

Value

A data frame holding distribution data.

List cohorts

Description

Extracts the data frame with limited cohort data columns.

Usage

cb_list_cohorts(size = 10, cb_version = "v2")

Arguments

size

Number of cohort entries from database. (Optional) Default - 10

cb_version

cohort browser version. ["v1" | "v2"] (Optional) Default - "v2"

Value

A data frame with available cohorts.

Examples

## Not run: 
cohorts_list()

## End(Not run)

Get cohort information

Description

Get all the details about a cohort including applied query.

Usage

cb_load_cohort(cohort_id, cb_version = "v2")

Arguments

cohort_id

Cohort id (Required)

cb_version

cohort browser version (Optional) [ "v1" | "v2" ]

Value

A cohort object.

See Also

cb_create_cohort for creating a new cohort.

Participant Count

Description

Returns the number of participants in a cohort if the supplied query were to be applied.

Usage

cb_participant_count(cohort, query = list(), keep_query = TRUE)

Arguments

cohort

A cohort object. (Required) See constructor function cb_create_cohort or cb_load_cohort

query

A phenotype query defined using the codephenotype function and logic operators (see example below)

keep_query

Apply newly specified query on top of exisiting query (Default: TRUE)

Value

A list with count of participants in the cohort and the total no. of participants in the dataset.

Plot filters

Description

Get a list of ggplot objects, each plot having one filter.

Usage

cb_plot_filters(cohort)

Arguments

cohort

A cohort object. (Required) See constructor function cb_create_cohort or cb_load_cohort

Value

A list of ggplot objects

Examples

## Not run: 
my_cohort <- cb_load_cohort(cohort_id = "5f9af3793dd2dc6091cd17cd")
plot_list <- cb_plot_filters(cohort = my_cohort)

plot_list[[1]]

library(ggpubr)
ggpubr::ggarrange(plotlist = plot_list)

## End(Not run)

Search available phenotypes

Description

Search for phenotypes in the Cohort Browser that match your term and return a tibble containing the metadata information for each matching phenotype. Use ' term = "" ' to return all phenotypes.

Usage

cb_search_phenotypes(term, cb_version = "v2")

Arguments

term

A term to search. (Required)

cb_version

cohort browser version (Optional) [ "v1" | "v2" ]

Value

A tibble with phenotype metadata

Examples

## Not run: 
cancer_phenos <- cb_search_phenotypes(term = "cancer")

all_phenos <- cb_search_phenotypes(term = "")

## End(Not run)

Set the columns in a cohort

Description

Updates a cohort by applying a new query.

Usage

cb_set_columns(cohort, column_ids, keep_columns = TRUE)

Arguments

cohort

A cohort object. (Required) See constructor function cb_create_cohort or cb_load_cohort

column_ids

Vector of phenotype IDs to be added as columns in the participant table.

keep_columns

If True, pre-existing columns are retained and newly supplied columns are added. Otherwise, pre-exisitng columns are overwritten. (Default: TRUE)

Value

The updated cohort object.

Examples

## Not run: 
my_cohort <- cb_load_cohort(cohort_id = "612f37a57673ed0ddeaf1333", cb_version = "v2")

my_cohort <- cb_set_columns(my_cohort, c(1, 99, 38), keep_columns = F)

## End(Not run)

Configure cloudos

Description

On a system for the first time the cloudos configuration needed to be done. This function can help do that.

Usage

cloudos_configure(base_url, token, team_id)

Arguments

base_url

Base URL for cloudos

token

API key or token

team_id

team/workspace ID

Value

None

whoami

Description

To check the current configuration

Usage

cloudos_whoami()

Value

None

cohort class

Description

This class creates a cohort object, which holds the information related to a cohort: cohort ID, name, description, query, table columns. This class is used in functions which carry out operations related to specific cohorts. A cohort class object can be created using constructor functions cb_create_cohort or cb_load_cohort.

Slots

id

cohort ID.

name

cohort name.

desc

cohort description.

phenoptype_filters

phenotypes displayed in the cohort overview.

query

applied query.

query_phenotype_ids

IDs of phenotypes used in the query.

columns

All the columns.

num_participants

number of participants in the cohort.

cb_version

chort browser version.

Define a phenotype

Description

Defines a single phenotype

Usage

phenotype(id, value, from, to, instance = "0")

Arguments

id

A single phenotype id. Possible phenotyoes can be explored using the codecb_search_phenotypes function

value

The categorical value of the phenotype id defined

from

For continuous phenotypes, the lower bound of the desired value range

to

For continuous phenotypes, the upper bound of the desired value phenotype

instance

The instance number of the phenotype, default 0

Value

A single phenotypes definition that cam be combined using &,| and ! operators

Examples

## Not run: 
continuous_phenotype <- phenotype(id = 13, from = "2016-01-21", to = "2017-02-13")
categorical_phenotype <- phenotype(id = 4, value = "Cancer")

## End(Not run)