getExperiment: Get PDX experiment data

In bhklab/Xeva: Analysis of patient-derived xenograft (PDX) data

Get PDX experiment data

Description

For a given model.id, getExperiment will

Usage

getExperiment(
  object,
  model.id = NULL,
  batch = NULL,
  patient.id = NULL,
  drug = NULL,
  control.name = NULL,
  treatment.only = FALSE,
  max.time = NULL,
  vol.normal = FALSE,
  log.volume = FALSE,
  return.list = FALSE,
  impute.value = FALSE,
  concurrent.time = FALSE
)

## S4 method for signature 'XevaSet'
getExperiment(
  object,
  model.id = NULL,
  batch = NULL,
  patient.id = NULL,
  drug = NULL,
  control.name = NULL,
  treatment.only = FALSE,
  max.time = NULL,
  vol.normal = FALSE,
  log.volume = FALSE,
  return.list = FALSE,
  impute.value = FALSE,
  concurrent.time = FALSE
)

Arguments

object	The XevaSet object.
model.id	The model.id for which data is required, multiple IDs are allowed.
batch	Batch name from the XevaSet or experiment design.
patient.id	Patient id from the XevaSet. Default NULL.
drug	Name of the drug.
control.name	Name of drug used as control. Default NULL.
treatment.only	Default FALSE. If TRUE, give data for non-zero dose periods only (if dose data are available).
max.time	Maximum time for data.
vol.normal	If TRUE it will normalize the volume. Default FALSE.
log.volume	If TRUE log of the volume will be used. Default FALSE.
return.list	Default FALSE will return a data.frame.
impute.value	Default FALSE. If TRUE, impute the missing values.
concurrent.time	Default FALSE. If TRUE, cut the batch data such that control and treatment will end at same time point.

Value

a data.fram will all the the values stored in experiment slot

Examples

data(brca)

getExperiment(brca, model.id="X.6047.uned", treatment.only=TRUE)

getExperiment(brca, model.id=c("X.6047.uned", "X.6047.pael"), treatment.only=TRUE)

getExperiment(brca, batch="X-6047.paclitaxel", treatment.only=TRUE)

ed <- list(batch.name="myBatch", treatment=c("X.6047.LJ16","X.6047.LJ16.trab"),
             control=c("X.6047.uned"))

getExperiment(brca, batch=ed)

bhklab/Xeva documentation built on Nov. 30, 2024, 3:17 a.m.