gather.ExpressionSet: Convert an ExpressionSet object into tidy format

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

Description

Convert an ExpressionSet object into tidy format

Usage

## S3 method for class 'ExpressionSet'
gather(x, sample_ids = NULL, gene_ids = NULL,
  sample_col = "cellid", gene_col = "Symbol")

Arguments

x	An ExpressionSet
sample_ids	A vector of sample ids. Default is NULL (don't filter on sample id)
gene_ids	A vector of gene ids. Default is NULL (don't filter on gene id)
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 tall_df format

Examples

data('CCLEsmall', package='PharmacoGx')
eset <- CCLEsmall@molecularProfiles$rna
gather.ExpressionSet(eset, sample_ids=c('143B', '23132-87'), gene_ids=c('BRAF', 'EGFR') )
gather.ExpressionSet(eset, sample_ids=c('143B', '23132-87') )

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