make_response_vs_genetic_df.data.frame: Create a response_vs_genetic data frame from two tall data...

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

Description

Create a response_vs_genetic data frame from two tall data frames

Usage

## S3 method for class 'data.frame'
make_response_vs_genetic_df(df, df2 = NULL,
  sample_ids = NULL, gene_ids = NULL, data_types = NULL,
  compound_ids = NULL, endpoints = NULL, resp_ids = NULL)

Arguments

df	a data frame in tall_df format containing the genetic data (and response data if df2 not set)
df2	a data frame in either tall_df or resp_df format containing the response data. Default is NULL (just use df)
sample_ids	A vector of sample ids. Default is NULL (don't filter on sample id)
gene_ids	Gene ids in df. Default is NULL (don't filter on gene id)
data_types	Data type for genetic data. Default is NULL (don't filter on data type)
compound_ids	A vector of compound ids. Default is NULL (don't filter on compound id)
endpoints	A vector of endpoints. Default is NULL (don't filter on endpoint)
resp_ids	A vector of response ids. Default is NULL (don't filter on response id)

Value

a data frame in rvg_df format

Examples

data('CCLEsmall', package='PharmacoGx')

genetic_data <- gather_assay.PharmacoSet(CCLEsmall, sample_ids=PharmacoGx::cellNames(CCLEsmall),
  gene_ids = c('RBM5', 'LAP3', 'CFTR'), data_type = 'rna')
resp_data <- gather_response.PharmacoSet(CCLEsmall, sample_ids=PharmacoGx::cellNames(CCLEsmall),
                         resp_ids=c('AEW541', 'Nilotinib'), resp_col='ic50_published')

rvg_df <- make_response_vs_genetic_df.data.frame(df=genetic_data, df2=resp_data, sample_ids=PharmacoGx::cellNames(CCLEsmall), gene_ids='RBM5',
 data_types='rna', resp_ids='Nilotinib')
rvg_df

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