response: compute PDX response

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

compute PDX response

Description

response Computes the drug response of an individual PDX model or batch.

Usage

response(
  object,
  model.id = NULL,
  batch = NULL,
  res.measure = c("mRECIST", "slope", "AUC", "angle", "abc", "TGI", "lmm", "bmRECIST"),
  treatment.only = FALSE,
  max.time = NULL,
  impute.value = TRUE,
  min.time = 10,
  concurrent.time = FALSE,
  vol.normal = FALSE,
  log.volume = FALSE,
  verbose = TRUE
)

Arguments

object	Xeva object.
model.id	model.id for which the durg response is to be computed.
batch	batch.id or experiment design for which the drug response is to be computed.
res.measure	Drug response measure. See Details below
treatment.only	Default TRUE. If TRUE, give data for time>=0 and if FALSE, uses all avaliable data.
max.time	Maximum time for data.
impute.value	Default FALSE. If TRUE, impute the missing values.
min.time	Default 10 days. Used for mRECIST computation.
concurrent.time	Default FALSE. If TRUE, cut the batch data such that control and treatment will end at same time point.
vol.normal	If TRUE it will normalize the volume. Default FALSE.
log.volume	If TRUE log of the volume will be used for response calculation. Default FALSE
verbose	Default TRUE will print information.

Details

At present the following response measures are implemented

• mRECIST Computes mRECIST for individual PDX models

• slope Computes slope of the fitted individual PDX curves

• AUC Computes area under a PDX curve for individual PDX models

• angle Computes angle between treatment and control PDX curves

• abc Computes area between the treatment and control PDX curves

• TGI Computes tumor growth inhibition using treatment and control PDX curves

• lmm Computes linear mixed model (lmm) statistics for a PDX batch

• bmRECIST Computes mRECIST for control and treatment arms of a PDX batch

Value

Returns model or batch drug response object.

Examples

data(brca)
response(brca, model.id="X.1004.BG98", res.measure="mRECIST")

response(brca, batch="X-6047.paclitaxel", res.measure="angle")

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

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