cometh: The constructor function for CoMeth objects
In PeteHaitch/cometh: Analyse, manage and visualise co-methylation data.

Description Usage Arguments Value See Also

This is the general function to construct a CoMeth object. Users will generally use the read.comethylation function to construct a CoMeth object. The constructor allows for multiple samples in the same object by passing most arguments as a *List where each element of the *List corresponds to the arguments for a given sample. These multiple samples will then be appropriately combined into a single CoMeth object.

CoMeth(sample_names = CharacterList(), methylation_type = CharacterList(),
  counts = DataFrameList(), seqnames = RleList(), pos = DataFrameList(),
  seqinfo = Seqinfo(), strand = RleList(), colData = DataFrame(),
  exptData = SimpleList(), ..., verbose = FALSE)

`sample_names`	A `CharacterList` containing the names of the samples. Sample names must be unique.
`methylation_type`	A `CharacterList` storing the type of methylation loci for these m-tuples. `methylation_type` must be named and the names must match those given in `sample_names`. For each sample the possible values are "CG", "CHG", "CHH" or "CNN" or multiple values specified as a character vector, e.g. c("CG", "CHG") or c("CHG", "CG") for "CG/CHG" methylation. The `methylation_type` of the resulting `CoMeth` object is the union of this argument, e.g. if `methylation_type = list('sample1' = 'CG', 'sample2' = 'CHH')` then the `methylation_type` of the resulting `CoMeth` object is `CG/CHH`; this also gives a warning.
`counts`	A `DataFrameList`. `counts` must be named and the names must match those given in `sample_names`. The entries in each DataFrame corresponds to the number of times that particular co-methylation pattern (columns) was observed for that particular m-tuple (rows). Therefore, each DataFrame must have the same number of rows as its corresponding DataFrame in `pos` and have 2 ^ \code{m} columns. All samples must have the same m, that is, all DataFrames in `counts` must have the same number of columns. The column names of each DataFrame must match those given by `.make_m_tuple_names(m)`.
`seqnames`	a `RleList`. `seqnames` must be named and the names must match those given in `sample_names`. Each Rle is the `seqnames` of each m-tuple for that sample.
`pos`	A `DataFrameList`. `pos` must be named and the names must match those given in `sample_names`. The columns of each DataFrame must be: `seqnames`, `pos1`, ..., `posm`, where, for example, `posm` is `pos3` if `m` = 3. Therefore, the number of columns of each DataFrame is m, the size of the m-tuples, and the number of rows is equal to the number of m-tuples for that particular sample. All samples must have the same m, that is, all DataFrames in `pos` must have the same number of columns.
`seqinfo`	A `Seqinfo` object containing information about the reference genome of the samples. Only a single value is accepted because all samples must be mapped against the same reference genome. However, multiple genomes per sample are allowed in order to accommodate a spiked-in unmethylated genome (normally lambda phage), which is a common step in a bisulfite-sequencing protocol. NOTE: `seqinfo` is a required argument in order to construct a `CoMeth` object, whereas for many Bioconductor objects it is an optional argument.
`strand`	An optional `RleList` object containing the strand information of each m-tuple. WARNING: If `strand` is not supplied, all m-tuples in the resulting `CoMeth` object will have their strand set to `` to signify that the strand is unknown or irrelevant. WARNING*: m-tuples will not be combined across samples if they are on different strands.
`colData`	An optional `DataFrame` describing the samples. Row names must match the `sample_names`, otherwise an error is returned. `sample_names`.
`exptData`	An optional `SimpleList` of arbitrary content describing the overall experiment.
`...`	Additional arguments passed to the internal call to the `MTuples` constructor. See `MTuples` for details on what these might be.
`verbose`	A `logical(1)` indicating whether messages about data coercion during construction should be printed.

A CoMeth1 (if m = 1), CoMeth2 (if m = 2) or CoMeth3Plus (if m >= 3) object. All these are concrete subclasses of the VIRTUAL CoMeth class.

cat("TODO")

read.comethylation for a function to read in the .tsv output file of comethylation and construct a CoMeth object.

SummarizedExperiment for the class that CoMeth extends.

PeteHaitch/cometh documentation built on May 8, 2019, 1:32 a.m.