metadata_get: Get metadata from ExpressionSet

In BCMSLab/rkip: Gene co-expression analysis of RKIP, autophagy and EMT in prostate cancer

Description

Get the metadata associated with an ExpressionSet object. This could be the phenotype or the features data. In either cases the functions uses the standard bioconductor accessor with some formating

Usage

metadata_get(eset, col_name, new_name, type = "phenotype")

Arguments

eset	An ExpressionSet object
col_name	A character vector of columns in the metadata
new_name	A character string of the new names of the columns
type	A character string (default 'phenotype')

Value

A data.frame always contains a column for each col_name with the name in new_name. When type is 'phenotype', row.names are the samples, and when type is 'features', row.names are the feature IDs/probes

Examples

library(Biobase)
data("sample.ExpressionSet")

metadata_get(sample.ExpressionSet,
             c('sex', 'type'),
             c('sex', 'type'))

BCMSLab/rkip documentation built on May 17, 2019, 2:14 a.m.