Package 'pogos'

subscripting on DRProfSet extracts a profile for a single drug whose name constitutes the index

Description

subscripting on DRProfSet extracts a profile for a single drug whose name constitutes the index

Usage

## S4 method for signature 'DRProfSet,character,ANY,ANY'
x[i, j, ..., drop = TRUE]

Arguments

x	instance of DRProfSet
i	character(1) drug name
j	not used
...	not used
drop	logical(1) not used

Value

a DRProfSet instance restricted to experiments involving the selected drug

---

convert binary output of GET()$content to list

Description

convert binary output of GET()$content to list

Usage

basicDecoder(x)

Arguments

x	string suitable for input to GET as GET(x)

Value

output of fromJSON, typically a list

Examples

cl = basicDecoder('https://pharmacodb.pmgenomics.ca/api/v1/cell_lines')
unlist(cl)

---

compounds_v1: serialization of compounds info from PharmacoDb v1

Description

compounds_v1: serialization of compounds info from PharmacoDb v1

Usage

compounds_v1

tissues_v1

cell_lines_v1

datasets_v1

CCLE_drts

Format

S4Vectors DataFrame instance

S4Vectors DataFrame instance

S4Vectors DataFrame instance

S4Vectors DataFrame instance

DRTraceSet instance

Source

PharmacoDb Sept 2017

PharmacoDb Sept 2017

PharmacoDb Sept 2017

PharmacoDb Sept 2017

PharmacoDb April 2018

Examples

data(compounds_v1)
head(compounds_v1)
data(tissues_v1)
head(tissues_v1)
data(cell_lines_v1)
head(cell_lines_v1)
data(datasets_v1)
head(datasets_v1)
data(CCLE_drts)
CCLE_drts

---

initial version of compound browser over pharmacoDb cells

Description

initial version of compound browser over pharmacoDb cells

Usage

compoundsByCell()

Value

only used for side effect of running shiny app

Note

Simple shiny app demonstrating coverage of PharmacoDb compounds by CHEBI. If a cell line selected is not present in selected dataset, the app will wait for a compatible selection to be made.

Examples

if (!requireNamespace("shiny")) stop("install shiny to use compoundsByCell")
if (interactive()) print(compoundsByCell())

---

DRProfSet is a class for managing dose-response information about cell lines from a pharmacogenomics dataset

Description

DRProfSet is a class for managing dose-response information about cell lines from a pharmacogenomics dataset

getDrugs extracts drug list

DRProfSet manages all data from a given cell line from a pharmacogenomics source

Usage

getDrugs(x)

DRProfSet(cell_line = "MCF7", dataset = "CCLE")

## S4 method for signature 'DRProfSet,missing'
plot(x, y, ...)

Arguments

x	instance of DRProfSet
cell_line	character(1) cell line name, entries in cell_lines_v1
dataset	character(1) resource name, entries in datasets_v1
y	for plot: not used
...	not used

Value

getDrugs: character vector

instance of DRProfSet

Examples

if (interactive()) trs = DRTraceSet() else trs = iriCCLE()
ps = traces(trs)[[1]]
ps
getDrugs(ps)
if (interactive()) DRProfSet()

---

DRTraceSet class manages dose-response information for a single cell line, multiple drugs

Description

DRTraceSet class manages dose-response information for a single cell line, multiple drugs

DRTraceSet constructor for multiple cell lines, single drug, single dataset

Usage

## S4 method for signature 'DRTraceSet,missing'
plot(x, y, ...)

DRTraceSet(
  cell_lines = c("SK-ES-1", "TC-71", "MHH-ES-1", "HCC-56", "SK-HEP-1"),
  drug = "Irinotecan",
  dataset = "CCLE"
)

Arguments

x	for plot: instance of DRTraceSet
y	for plot: not used
...	not used
cell_lines	character vector of cell line names, must be found in 'cell_lines_v1' data of pogos package
drug	character(1) drug name in 'compounds_v1'
dataset	character(1) dataset known to pharmacodb.pmgenomics.ca

Value

instance of DRTraceSet

Note

Will query pharmacodb for relevant dose-response information

Examples

DRTraceSet()

---

obtain an example trace set stored locally, for irinotecan and selected cell lines

Description

obtain an example trace set stored locally, for irinotecan and selected cell lines

Usage

iriCCLE()

Value

an instance of DRTraceSet

Examples

iri = iriCCLE()
iri
plot(iri)

---

very simple query formulation, build queries using endpoints of bhklab PharmacoDB API

Description

very simple query formulation, build queries using endpoints of bhklab PharmacoDB API

Usage

rxdbQuery_v1(
  ...,
  url = "https://pharmacodb.pmgenomics.ca/api/v1/",
  decoder = basicDecoder
)

Arguments

...	typically a string representing an API endpoint, will be processed by unlist() and then to paste0 preceded by url
url	of a PharmacoDB server API target
decoder	a function of one argument that will be applied to API response (typically JSON)

Value

typically a list, dependent on decoder parameter

Examples

qout = rxdbQuery_v1('cell_lines') # yields 30; append '?all=true' to retrieve all
unlist(lapply(qout, function(x) x[[2]]))

---

enumerate top level endpoint terms for bhklab PharmacoDB API

Description

enumerate top level endpoint terms for bhklab PharmacoDB API

Usage

topEndpoints_v1()

Value

a character vector of available endpoints

Examples

topEndpoints_v1()

---

trace extractor

Description

trace extractor

Usage

traces(x)

Arguments

x	instance of DRTraceSet

Value

a list of DRProfile instances

Examples

iri = iriCCLE()
str(traces(iri)[[1]])

---