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

getExperiment

R Documentation

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 time>=0 only.
`max.time`	Maximum time for data.
`vol.normal`	Default `FALSE` will return raw volume. If TRUE it will normalize the volume by treatment start volume (volume at time>=0). If set to `'all'` will use full data to volume normalization.
`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. 12, 2022, 5:38 a.m.