combogds: Combine two different gds objects.

Description Usage Arguments Details Value Note Author(s) Examples

Description

Combines the shared gdsn.class nodes between two gds objects depending on primary gds.object dimensions.

Usage

1
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.

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

Value

a new gds object that has both files within it

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 <[email protected]>

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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")

bigmelon documentation built on May 2, 2018, 3:18 a.m.