DESeqAnalysis | R Documentation |
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
.
DESeqAnalysis(data, transform, results, lfcShrink = NULL)
data |
|
transform |
|
results |
|
lfcShrink |
|
DESeqAnalysis
.
Updated 2021-03-15.
data <- DESeq2::makeExampleDESeqDataSet() rowRanges <- AcidGenomes::emptyRanges(names = rownames(data)) mcols(rowRanges)[["geneId"]] <- paste0("id", seq_len(length(rowRanges))) mcols(rowRanges)[["geneName"]] <- paste0("name", seq_len(length(rowRanges))) rowRanges(data) <- rowRanges data <- DESeq2::DESeq(data) class(data) transform <- DESeq2::varianceStabilizingTransformation(data) class(transform) resultsNames(data) name <- resultsNames(data)[[2L]] results <- DESeq2::results(data, name = name) class(results) lfcShrink <- DESeq2::lfcShrink(dds = data, res = results, coef = 2L) results <- list(results) names(results) <- name lfcShrink <- list(lfcShrink) names(lfcShrink) <- name object <- DESeqAnalysis( data = data, transform = transform, results = results, lfcShrink = lfcShrink ) print(object)
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