combogds: Combine two different gds objects together

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

Combine two different gds objects together

Description

Function will attempt to combine together the shared gdsn.class nodes between two gds object depending on the dimensions of the primary gds.class object.

Usage

combo.gds(file, primary, secondary)

Arguments

file	Name of the new gds file to be created.
primary	A gds.class object.
secondary	A gds.class object.

Details

–EXPERIMENTAL– Will crudely combine shared nodes between primary and secondary based on the dimensions / rownames of the primary node. NAs will be coerced where probes are missing from secondary gds.

Currently will only look for nodes with the names "betas", "methylated", "unmethylated", "pvals" and "NBeads".

Value

Returns (and creates) as new gds file in the specified location with the combination of two gds objects together.

Note

Will lose information relating to "pData". Therefore we recommend compiling separate pData object manually and adding combined pData post-function

Author(s)

Tyler Gorrie-Stone <[e-mail]>

Examples

data(melon)
a <- es2gds(melon[,1:6], "primary.gds")
b <- es2gds(melon[,7:12], "secondary.gds")

ab <- combo.gds("combo.gds", primary = a, secondary = b)

closefn.gds(a)
unlink("primary.gds")
closefn.gds(b)
unlink("secondary.gds")
closefn.gds(ab)
unlink("combo.gds")

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