batchInfo: Get batch information

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

Get batch information

Description

Get batch information from a Xeva dataset.

Usage

batchInfo(
  object,
  batch = NULL,
  model.id = NULL,
  model.id.type = c("any", "control", "treatment"),
  other.col = NULL,
  return.df = FALSE
)

Arguments

object	The Xeva object from which batch information is obtained.
batch	Name of the batch. Default NULL.
model.id	Model ID for which need to be searched in the batches. Default NULL.
model.id.type	Type of the model ID in a batch. See the Details section below.
return.df	If TRUE, will return a data.frame (see the Details). Default FALSE.
patient.id	If TRUE, will return patient.id . Default FALSE.
drug	If TRUE, will return drug . Default FALSE.

Details

By default this function will return the names of all the batches present in the dataset. If a batch specified, it will return the experiment design (control and treatment model IDs) of that particular batch. If model.id is specified, it will return the names of all the batches where this particuler model.id is present. If both batch and model.id are specified, batch will take precedent.

For model.id.type, the default value 'any' will return all the batch IDs where the given model ID is present in any arm (ie. control or treatment) of the batch. It can also be restricted to look only for treatment (or control) arm by specifying the type.

If return.df=TRUE, it will return a data.frame where each batch will be a row. Multiple model.ids will be merged by ; . It will also return patient.id and drug.

Value

A Vector with batch names.

Examples

data(brca)
##to get all the batch names
batch.name <- batchInfo(brca)

##to get a specific batch
batch.design <- batchInfo(brca, batch=batch.name[1])

##to get all the batches where a model.id is present in control arm
bn <- batchInfo(brca, model.id="X.6047.uned", model.id.type="control")

##get batch level information with tissue column added
batch.name <- batchInfo(brca)
batch.df <- batchInfo(brca, batch=batch.name[1:10], other.col="tissue",return.df = TRUE)

bhklab/Xeva documentation built on Nov. 12, 2022, 5:38 a.m.