make_genetic_vs_genetic_df.PharmacoSet: Create a genetic_vs_genetic data frame from the data in a...

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

Description

Create a genetic_vs_genetic data frame from the data in a PharmacoSet

Usage

## S3 method for class 'PharmacoSet'
make_genetic_vs_genetic_df(x, sample_ids = NULL, gene1,
  gene2, data_type1, data_type2, sample_col = "cellid",
  gene_col1 = "Symbol", gene_col2 = "Symbol")

Arguments

x	PharmacoSet object
sample_ids	A vector of sample ids. Default is NULL (don't filter on sample id)
gene1	First gene(s)
gene2	Second gene(s)
data_type1	Data type for gene 1
data_type2	Data type for gene 2
sample_col	Name of the column in the pData data frame to use for filtering on sample id
gene_col	Name of the column in the rowData data frame to use for filtering on gene id

Value

a data frame in gvg_df format

Examples

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

gvg_df <- make_genetic_vs_genetic_df.PharmacoSet(CCLEsmall, sample_ids=PharmacoGx::cellNames(CCLEsmall), gene1='RBM5', gene2='RBM5',
 data_type1='rna', data_type2='rnaseq', gene_col1 = "Symbol", gene_col2 = "gene_name")
gvg_df

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