DESeqDataSet-class {DESeq2} | R Documentation |
The 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, ...)
se |
a |
design |
a formula which specifies the design of the
experiment, taking the form |
countData |
for matrix input: a matrix of non-negative integers |
colData |
for matrix input: a |
sampleTable |
for htseq-count: a |
directory |
for htseq-count: the directory relative to which the filenames are specified |
ignoreRank |
for advanced use only, allows creation of a DESeqDataSet which is not of full rank |
... |
arguments provided to
|
A DESeqDataSet object.
See http://www-huber.embl.de/users/anders/HTSeq for htseq-count
countData <- matrix(1:4,ncol=2) colData <- data.frame(condition=factor(c("a","b"))) dds <- DESeqDataSetFromMatrix(countData, colData, formula(~ condition))