getrg: Query and store data from h5 file signal tables

In metamaden/recountmethylation: Access and analyze public DNA methylation array data compilations

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"

metamaden/recountmethylation documentation built on Jan. 5, 2023, 9:56 a.m.