DESeqDataSet: DESeqDataSet object and constructors

In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution

Description

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.

Usage

DESeqDataSet(se, design, ignoreRank = FALSE)

DESeqDataSetFromMatrix(countData, colData, design, tidy = FALSE,
  ignoreRank = FALSE, ...)

DESeqDataSetFromHTSeqCount(sampleTable, directory = "", design,
  ignoreRank = FALSE, ...)

Arguments

se	a 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.
design	a formula which expresses how the counts for each gene depend on the variables in colData. Many R formula are valid, including designs with multiple variables, e.g., ~ group + condition, and designs with interactions, e.g., ~ genotype + treatment + genotype:treatment. See results for a variety of designs and how to extract results tables. By default, the functions in this package will use the last variable in the formula for building results tables and plotting.
ignoreRank	use of this argument is reserved for DEXSeq developers only. Users will immediately encounter an error upon trying to estimate dispersion using a design with a model matrix which is not full rank.
countData	for matrix input: a matrix of non-negative integers
colData	for matrix input: a DataFrame or data.frame with at least a single column. Rows of colData correspond to columns of countData
tidy	for matrix input: whether the first column of countData is the rownames for the count matrix
...	arguments provided to SummarizedExperiment including rowRanges and exptData. Note that for Bioconductor 3.1, rowRanges must be a GRanges or GRangesList, with potential metadata columns as a DataFrame accessed and stored with mcols. If a user wants to store metadata columns about the rows of the countData, but does not have GRanges or GRangesList information, first construct the DESeqDataSet without rowRanges and then add the DataFrame with mcols(dds).
sampleTable	for htseq-count: a data.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 colData
directory	for htseq-count: the directory relative to which the filenames are specified

Value

A DESeqDataSet object.

References

See http://www-huber.embl.de/users/anders/HTSeq for htseq-count

Examples

countData <- matrix(1:100,ncol=4)
condition <- factor(c("A","A","B","B"))
dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ condition)

nlhuong/ZeroInflatedDESeq2 documentation built on May 23, 2019, 9:06 p.m.