A call to expressionSet class — make_ExpressionSet • pQTLtools

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.

Value

An ExpressionSet object.

Details

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

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))
#> [1] TRUE
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="pfermat@lab.not.exist",
    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)
#> [1] FALSE
invisible(Biobase::esApply(exampleSet,2,hist))


























lm(score~gender+X31739_at,data=exampleSet)
#> 
#> Call:
#> lm(formula = score ~ gender + X31739_at, data = exampleSet)
#> 
#> Coefficients:
#> (Intercept)   genderMale    X31739_at  
#>   0.6006673    0.0108515   -0.0003012  
#>