getrg {recountmethylation} | R Documentation

## Query and store data from h5 file signal tables

### Description

Queries signal datasets in an h5 HDF5 database file. Handles identity queries to rows (GSM IDs) or columns (bead addresses). Returns query matches either as a list of datasets or a single RGChannelSet, with option to include sample metadata.

### Usage

    getrg(
      dbn,
      gsmv = NULL,
      cgv = NULL,
      data.type = c("se"),
      dsv = c("redsignal", "greensignal"),
      all.gsm = FALSE,
      all.cg = TRUE,
      metadata = TRUE,
      md.dsn = "mdpost",
      verbose = FALSE
    )

### Arguments

`dbn` | Name of the HDF5 database file.
`gsmv` | Vector valid GSM IDs (rows) to query, either NULL or vector of length > 2 valid GSM IDs, or "all.gsm" should be TRUE.
`cgv` | Vector of valid bead addresses (columns) to query in the signal datasets (default NULL).
`data.type` | Format for returned query matches, either as datasets "df" or RGChannelSet "se" object.
`dsv` | Vector of raw signal datasets or group paths to query, including both the red channel 'redsignal' and green channel 'greensignal' datasets.
`all.gsm` | Whether to query all available GSM IDs.
`all.cg` | Whether to query all available CpG probe addresses.
`metadata` | Whether to access available postprocessed metadata for queried samples.
`md.dsn` | Name of metadata dataset in h5 file.
`verbose` | Whether to post status messages.

### Value

Returns either an RGChannelSet or list of data.frame objects from dataset query matches.

### See Also

rgse()

### Examples

    path <- system.file("extdata", "h5test", package = "recountmethylation")
    fn <- list.files(path)
    dbpath <- file.path(path, fn)
    rg <- getrg(dbn = dbpath, all.gsm = TRUE, metadata = FALSE)
    dim(rg) # [1] 11162     2
    class(rg)
    # [1] "RGChannelSet"
    # attr(,"package")
    # [1] "minfi"

[Package recountmethylation version 1.0.0 Index]