getrg: Query and store data from h5 file signal tables

View source: R/accessors.R

getrgR 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"

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