redirect.gds {bigmelon}R Documentation

Change the location of file 'paths' for row and column names.

Description

Quickly change contents of gdsn.class node "paths".

Usage

redirect.gds(gds, rownames, colnames)

Arguments

gds

gds.class object containing node named "paths".

rownames

Character string that points to named part of supplied gds that corresponds to rownames. e.g. "fData/Target_ID". Default = "fData/Probe_ID"

colnames

Character string that points to names part of supplied gds that corresponds to colnames. e.g. "pData/Sample_ID". Default = "pData/barcode"

Details

Function is important within many functions and can lead to errors if row and column names are not correctly specified. By default, es2gds can recognize whether a methylumiset object was read in through readEPIC or methylumiR and will set the row and col names paths correctly. Will fail noisily if given a pathway that does not exist.

Value

Changes the gdsn.class object named "paths" to supplied rownames and colnames within supplied gds.class object.

Author(s)

Tyler J. Gorrie-Stone Who to contact: <tgorri@essex.ac.uk>

See Also

add.gdsn, app2gds, es2gds

Examples

data(melon)
e <- es2gds(melon, "melon.gds") # Create gds object
redirect.gds(e, rownames = "fData/TargetID", colnames = "pData/sampleID")
# Deleting Temp files
closefn.gds(e)
unlink("melon.gds")


[Package bigmelon version 1.10.0 Index]