make_ExpressionSet | R Documentation |
This is really a direct call to the Bioconductor/Biobase class.
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),
...
)
assayData |
Expression data. |
phenoData |
Phenotype. |
featureData |
featureData. |
experimentData |
Information on data source. |
annotation |
Annotation information. |
protocolData |
protocol information. |
... |
Other options. |
The explicit call make it easier to handle proteomic data for other downstream analyses.
An ExpressionSet object.
Adapted from Bioconductor/Biobase following a number of proteomic pilot studies.
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="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)
invisible(Biobase::esApply(exampleSet,2,hist))
lm(score~gender+X31739_at,data=exampleSet)
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