make_genetic_vs_genetic_df.data.frame: Create a genetic_vs_genetic data frame from two tall data...

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

Description

Create a genetic_vs_genetic data frame from two tall data frames

Usage

## S3 method for class 'data.frame'
make_genetic_vs_genetic_df(df, df2 = NULL,
  sample_ids = NULL, gene1 = NULL, gene2 = NULL, data_type1 = NULL,
  data_type2 = NULL)

Arguments

df	a data frame in tall_df format containing genetic data for feature 1 (and feature 2 if df2 is NULL)
df2	a data frame in tall_df format containing genetic data for feature 2 Default is NULL (just use df)
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')

dat1 <- gather_assay.PharmacoSet(CCLEsmall, sample_ids=PharmacoGx::cellNames(CCLEsmall),
  gene_ids = c('RBM5', 'LAP3', 'CFTR'), data_type = 'rna')
dat2 <- gather_assay.PharmacoSet(CCLEsmall, sample_ids=PharmacoGx::cellNames(CCLEsmall),
  gene_ids = c('RBM5', 'LAP3', 'CFTR'), data_type = 'rnaseq', gene_col='gene_name')

gvg_df <- make_genetic_vs_genetic_df.data.frame(df=dat1, df2=dat2, sample_ids=PharmacoGx::cellNames(CCLEsmall), gene1='RBM5', gene2='RBM5',
 data_type1='rna', data_type2='rnaseq')
gvg_df

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