DESeqDataSet is a subclass of SummarizedExperiment,
used to store the input values, intermediate calculations and results of an
analysis of differential expression. The DESeqDataSet class
enforces non-negative integer values in the "counts" matrix stored as
the first element in the assay list.
In addition, a formula which specifies the design of the experiment must be provided.
The constructor functions create a DESeqDataSet object
from various types of input:
a SummarizedExperiment, a matrix, or count files generated by
the python package HTSeq. See the vignette for examples of construction
from all three input types.
DESeqDataSet(se, design, ignoreRank = FALSE)
DESeqDataSetFromMatrix(countData, colData, design, ignoreRank = FALSE, ...)
DESeqDataSetFromHTSeqCount(sampleTable, directory = "", design, ignoreRank = FALSE, ...)SummarizedExperiment with at least one column in colData,
and the counts as the first element in the assays list, which will be renamed
"counts". A SummarizedExperiment object can be generated by the
function summarizeOverlaps in the GenomicRanges package.formula(~ x + y + z). By default, the functions in this package will use
the last variable in the formula (e.g. z) for presenting results (fold changes, etc.) and plotting.DataFrame or data.frame with at least a single column.
Rows of colData correspond to columns of countData.SummarizedExperiment including rowData and exptDatadata.frame with three or more columns. Each row
describes one sample. The first column is the sample name, the second column
the file name of the count file generated by htseq-count, and the remaining
columns are sample metadata which will be stored in colDatacountData <- matrix(1:4,ncol=2)
colData <- data.frame(condition=factor(c("a","b")))
dds <- DESeqDataSetFromMatrix(countData, colData, formula(~ condition))
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