make_ExpressionSet: A call to expressionSet class

In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

A call to expressionSet class

Description

This is really a direct call to the Bioconductor/Biobase class.

Usage

make_ExpressionSet(
  assayData,
  phenoData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  featureData = Biobase::annotatedDataFrameFrom(assayData, byrow = TRUE),
  experimentData = Biobase::MIAME(),
  annotation = character(),
  protocolData = Biobase::annotatedDataFrameFrom(assayData, byrow = FALSE),
  ...
)

Arguments

assayData	Expression data.
phenoData	Phenotype.
featureData	featureData.
experimentData	Information on data source.
annotation	Annotation information.
protocolData	protocol information.
...	Other options.

Details

The explicit call make it easier to handle proteomic data for other downstream analyses.

Value

An ExpressionSet object.

Note

Adapted from Bioconductor/Biobase following a number of proteomic pilot studies.

Examples

dataDirectory <- system.file("extdata", package="Biobase")
exprsFile <- file.path(dataDirectory, "exprsData.txt")
exprs <- as.matrix(read.table(exprsFile, header=TRUE, sep="\t", row.names=1, as.is=TRUE))
pDataFile <- file.path(dataDirectory, "pData.txt")
pData <- read.table(pDataFile, row.names=1, header=TRUE, sep="\t")
all(rownames(pData)==colnames(exprs))
metadata <- data.frame(labelDescription=
                       c("Patient gender",
                         "Case/control status",
                         "Tumor progress on XYZ scale"),
                       row.names=c("gender", "type", "score"))
suppressMessages(library(Biobase))
phenoData <- Biobase::AnnotatedDataFrame(data=pData, varMetadata=metadata)
experimentData <- Biobase::MIAME(
    name="Pierre Fermat",
    lab="Francis Galton Lab",
    contact="[e-mail]",
    title="Smoking-Cancer Experiment",
    abstract="An example ExpressionSet",
    url="www.lab.not.exist",
    other=list(notes="Created from text files"))
exampleSet <- pQTLtools::make_ExpressionSet(exprs,phenoData,
                                 experimentData=experimentData,
                                 annotation="hgu95av2")
data(sample.ExpressionSet, package="Biobase")
identical(exampleSet,sample.ExpressionSet)
invisible(Biobase::esApply(exampleSet,2,hist))
lm(score~gender+X31739_at,data=exampleSet)

jinghuazhao/pQTLtools documentation built on June 11, 2025, 12:03 p.m.