readData2eset: Create ExpressionSet object from expression data

Description Usage Arguments Details Value Author(s)

View source: R/GEX_readData2eset.R

Description

ExpressionSet object assembled from expression, feature and phenotype data.

Usage

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readData2eset(
  exprsData,
  phenoData,
  featureData = NULL,
  ProbeID = "PROBE_ID",
  sampleColumn = "Sample_Name",
  groupColumn = "Sample_Group",
  experimentData = MIAME(),
  annotation = character(),
  transform = log2
)

Arguments

exprsData

dataframe or character with filepath to expression data to be loaded. If no rownames are included, a column containing ProbeIDs is expected and used as feature names.

phenoData

dataframe or character with filepath to sample sheet / phenotype data to be loaded.

featureData

dataframe or character with filepath to feature data to be loaded. If NULL, non-numeric data columns from 'exprsData' are used as feature data (if any).

ProbeID

character with name of the column in 'exprsData' and 'featureData' that contains identifiers used to uniquely identify each probe.

sampleColumn

character with name of sample column in 'phenoData'.

groupColumn

character with name of group column in 'phenoData'.

experimentData

MIAME object with optional experiment description.

annotation

character string specifying array annotation package (e.g. "Humanv4"). character() if not available.

transform

optional function definition to transform expression data (e.g. log2 for logarithm of base 2). if NULL, no data transformation is performed.

Details

Expression data, phenotype data and optional feature data are used to make an ExpressionSet object. Only numeric columns in exprsData are used. If no feature data is given, non-numeric data columns from exprsData are used as feature data (if any). If dataframes don't contain rownames as identifier, the column ProbeID is used as rownames in exprsData and featureData and column sampleColumn in phenoData. Rownames of exprsData must match with rownames of featureData (if given). Column names of exprsData must match with rownames of phenoData. Characters "/" and "-" in sample names or group names are replaced by ".". If either gene symbols or EntrezIDs are missing in feature data, this annotation is added using the corresponding annotation package if available (species name is derived from annotation). The optional function given in transform is used to transform the expression data.

Value

ExpressionSet object

Author(s)

Frank Ruehle


frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.