bigmelon-accessors {bigmelon} | R Documentation

## Bigmelon accessors

### Description

Functions to access data nodes in gds.class objects.

### Usage

    ## S4 method for signature 'gds.class'
    betas(object)
    ## S4 method for signature 'gds.class'
    methylated(object)
    ## S4 method for signature 'gds.class'
    unmethylated(object)
    ## S4 method for signature 'gds.class'
    pvals(object)
    ## S4 method for signature 'gds.class'
    fData(object)
    ## S4 method for signature 'gds.class'
    pData(object)
    ## S4 method for signature 'gds.class'
    QCmethylated(object)
    ## S4 method for signature 'gds.class'
    QCunmethylated(object)
    ## S4 method for signature 'gds.class'
    QCrownames(object)
    ## S4 method for signature 'gds.class'
    getHistory(object)
    ## S4 method for signature 'gds.class'
    colnames(x, do.NULL=TRUE, prefix=NULL)
    ## S4 method for signature 'gds.class'
    rownames(x, do.NULL=TRUE, prefix=NULL)
    ## S4 method for signature 'gds.class'
    exprs(object)
    ## S4 method for signature 'gds.class'
    fot(x)

### Arguments

`object` | A gds.class object.

for colnames and rownames:

`x` | A gds.class object.
`do.NULL` | logical. If 'FALSE' and names are 'NULL', names are created.
`prefix` | prefix: for created names.

### Details

Each function will return the data stored in the corresponding node as either a gdsn.class object, matrix, or data.frame. These are names following the conventions of the methylumi package and perform similar functions.

Each function which returns a gdsn.class object can be further index using the '[' operators. This includes an additional name argument which optionally returns the named attributes to the data as these are not stored inside the gdsn.node.

The QC functions will return the QC data as a matrix, these are seperated for methylation and unmethylated values and the rownames.

exprs will return a data.frame from beta values for all probes and all samples.

### Value

Returns specified node representing the called accessor

### Author(s)

Leonard C Schalkwyk, Ayden Saffari, Tyler Gorrie-Stone Who to contact: <t.gorrie-stone@qmul.ac.uk>

### Examples

    data(melon)
    e <- es2gds(melon,'wat_melon.gds')
    betas(e)
    head(betas(e)[,])
    methylated(e)[1:5, 1:3]
    unmethylated(e)[1:3 ,1:5]
    pvals(e)[1:5, 1:5]
    head(fData(e))
    head(pData(e))
    head(colnames(e))
    head(rownames(e))

    closefn.gds(e)
    unlink("wat_melon.gds")

[Package bigmelon version 1.20.0 Index]