redirect: Change the location of the paths for row and column names in...

In TJGorrie/bigmelon: Illumina methylation array analysis for large experiments

Change the location of the paths for row and column names in a gds file.

Description

Change how a gds object ascribes row and column names by changing the paths node of a gds file. Although a bit laborious, the row and column information is not preserved inside a node which contains data. Thusly during accession the row and column names are attributed after data has been accessed.

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

This function is particularly important within many functions inside bigmelon and may lead to downstream errors if the row and column names are not correctly specified. If data is read in through es2gds the path nodex should be correctly set up and all downstream analysis will carry out as normal. Will fail noisily if given a pathway that does not exist.

Value

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

Author(s)

Tyler J. Gorrie-Stone Who to contact: <[e-mail]>

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")

TJGorrie/bigmelon documentation built on June 12, 2024, 6:19 p.m.