update_eset.phenotype: Reassign the phenoData slot of ExpressionSet and Update...

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Reassign the phenoData slot of ExpressionSet and Update phenotype information

Description

update_eset.phenotype reassigns the phenoData slot of ExpressionSet based on user's demand. It is mainly used to modify sample names and extract interested phenotype information for further sample clustering.

Usage

update_eset.phenotype(
  use_eset = NULL,
  use_phenotype_info = NULL,
  use_sample_col = NULL,
  use_col = "auto"
)

Arguments

use_eset	ExpressionSet class object.
use_phenotype_info	data.frame, a dataframe contains phenotype information, can be obtained by calling pData function.
use_sample_col	character, must be one of the column names in use_phenotype_info.
use_col	character, the columns will be kept from use_phenotype_info. 'auto', only extracting 'cluster-meaningful' sample features (e.g. it is meaningless to use 'gender' as clustering feature, if all samples are female). 'GEO-auto' means it will extract the following selected columns, "geo_accession", "title", "source_name_ch1", and columns ended with ":ch1". Default is "auto".

Value

Return an ExressionSet object with updated phenotype information.

Examples

## Not run: 
net_eset <- load.exp.GEO(out.dir='./test',
                         GSE='GSE116028',
                         GPL='GPL6480',
                         getGPL=TRUE,
                         update=FALSE)
net_eset <- update_eset.phenotype(use_eset=net_eset,
                                  use_phenotype_info=Biobase::pData(net_eset),
                                  use_sample_col='geo_accession',
                                  use_col='GEO-auto')

## End(Not run)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.