app2gds: Append a MethyLumiSet object to a CoreArray Genomic Data...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/inout.R

Description

This function will append a MethyLumiSet data object to a CoreArray Genomic Data Structure(GDS) data file, and return as a gds.class object.

Usage

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app2gds(m, bmln)

Arguments

m

The MethyLumiSet object to be appended to the CoreArray Genomic Data Structure (GDS) data file

bmln

Either: A gds.class object

Or: A character string specifying the name of an existing .gds file to write to.

Or: A character string specifying the name of a new .gds file to write to

Details

Currently, the function only works with MethylumiSet objects and will produce unexpected results if the number of rows of the new objects does not match the existing .gds object. To prevent any errors from occuring it is recommended that raw .idat files are read in with readEPIC or appended iadd to ensure that all rows are the same length and have the same annotation.

Value

A gds.class object, which points to the appended .gds file.

Author(s)

Leonard C Schalkwyk, Ayden Saffari, Tyler Gorrie-Stone Who to contact: <tgorri@essex.ac.uk>

See Also

es2gds, iadd.

Examples

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#load example dataset
data(melon)

#split data into halves
melon_1 <- melon[,1:6]
melon_2 <- melon[,7:12]

#convert first half to gds
e <- es2gds(melon_1,'1_half_melon.gds')

#append second half to existing gds file
f <- app2gds(melon_2,e)

closefn.gds(e)
unlink("1_half_melon.gds")

bigmelon documentation built on May 31, 2017, 11:15 a.m.

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