app2gds: Append a MethyLumiSet object to a preexisting gds file

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

Append a MethyLumiSet object to a preexisting gds file

Description

This function will append a MethyLumiSet object to a gds file and return a gds.class object.

Usage

app2gds(m, bmln)

Arguments

m	The MethyLumiSet object to be appended to the gds file, with the same number of rows as the gds file.
bmln	Either: A gds.class object Or: A character string specifying the filepath of an existing .gds file to write to. Or: A character string specifying the file path of a new .gds file to write to

Details

Currently this function only takes a MethyLumiSet object as the only type of eligible input. This function will also produce unexpected results if the number of rows of the new object does not match the existing .gds file. Hopefully the function will noisily fail if this is the case however to prevent any errors from occuring it is recommended that raw idat files are read in using readEPIC or appended with iadd or iadd2 to ensure that all rows are of the same length and have the same annotation.

Value

A gds.class object pointed towards the newly appended .gds file.

Author(s)

Leonard C Schalkwyk, Ayden Saffari, Tyler Gorrie-Stone Who to contact: <[e-mail]>

See Also

es2gds, iadd, iadd2.

Examples

#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)

unlink("1_half_melon.gds")

TJGorrie/bigmelon documentation built on Oct. 13, 2023, 9:51 p.m.