gather_response.PharmacoSet: Convert response data from a PharmacoSet into tidy format

In chapmandu2/biotidyr: Tidy functions for MultiAssayExperiment and PharmacoGX objects

Description

Convert response data from a PharmacoSet into tidy format

Usage

## S3 method for class 'PharmacoSet'
gather_response(x, sample_ids = NULL, resp_ids = NULL,
  resp_col = "ic50_published", extra_cols = NULL)

Arguments

x	PharmacoSet object
sample_ids	A vector of sample ids. Default is NULL (don't filter on sample id)
resp_ids	A vector of response ids. Default is NULL (don't filter on response id)
resp_col	Response variable to retrieve
extra_cols	Optional additional columns to retrieve from the PharmacoSet drug info. Default is NULL

Value

a data frame in tall_df format

Examples

data('CCLEsmall', package='PharmacoGx')
gather_response.PharmacoSet(CCLEsmall, sample_ids=c('CHL-1', 'SW1573'),
                         resp_ids=c('AEW541', 'Nilotinib'),
                         resp_col='ic50_published')

gather_response.PharmacoSet(CCLEsmall, sample_ids=c('CHL-1', 'SW1573'),
                         resp_ids=c('AEW541', 'Nilotinib'),
                         resp_col='ic50_published', extra_cols='nbr.conc.tested')

chapmandu2/biotidyr documentation built on May 13, 2019, 3:29 p.m.