DESeqAnalysis-class: DESeq2 differential expression analysis

Description Usage Arguments Value Slots DESeqDataSet DESeqTransform DESeqResults Author(s) See Also Examples

Description

Class containing all elements generated during differential expression analysis with DESeq2. This class is essentially a list with validity checks to ensure DESeqTransform and DESeqResults correspond to the DESeqDataSet.

Usage

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Arguments

data

DESeqDataSet.

transform

DESeqTransform. DESeq2::varianceStabilizingTransformation() recommended by default.

results

list or single DESeqResults. One or more unshrunken DESeqResults. Assign the DESeq2::results() return here.

lfcShrink

listor single DESeqResults. One or more shrunken DESeqResults. Assign the DESeq2::lfcShrink() return here.

Value

DESeqAnalysis. Contains a DESeqDataSet, DESeqTransform, and corresponding DESeqResults list.

Slots

data

DESeqDataSet.

transform

DESeqTransform.

results

list. One or more unshrunken DESeqResults.

lfcShrink

list. Optional. One or more shrunken DESeqResults. If set, must correspond to those defined in results.

DESeqDataSet

We recommend generating the DESeqDataSet by coercion from bcbioRNASeq object using as(dds, "bcbioRNASeq"). Don't use the DESeq2::DESeqDataSet() or DESeq2::DESeqDataSetFromMatrix() constructors to generate the DESeqDataSet object.

DESeqTransform

Object containing variance-stabilized counts. We recommend slotting the return from either DESeq2::varianceStabilizingTransformation() or DESeq2::rlog().

DESeqResults

Don't modify any of the DESeqResults objects manually. This includes rearranging the rows or dropping genes without adjusted P values. We'll take care of this automatically in supported methods.

Author(s)

Michael Steinbaugh

See Also

Examples

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library(DESeq2)

data <- DESeq(makeExampleDESeqDataSet())
class(data)

transform <- varianceStabilizingTransformation(data)
class(transform)

resultsNames(data)
name <- resultsNames(data)[[2L]]
results <- results(data, name = name)
class(results)

lfcShrink <- lfcShrink(dds = data, res = results, coef = 2L)

results <- list(results)
names(results) <- name
lfcShrink <- list(lfcShrink)
names(lfcShrink) <- name
identical(names(results), names(lfcShrink))

x <- DESeqAnalysis(
    data = data,
    transform = transform,
    results = results,
    lfcShrink = lfcShrink
)
print(x)

steinbaugh/DESeqAnalysis documentation built on March 22, 2019, 5:51 p.m.