load_miRNA: Loading microarray miRNA data from a single experiment

In EwaMarek/FindReference: Find reference genes or miRNAs basing on microarray data.

Description

load_miRNA function loads data for a single miRNA microarray experiment. The only supported platform is Agilent.

Usage

load_miRNA(table, path)

Arguments

table	A character matrix with information about experiment. The row names of it should be the names of files with data and the column names should be 'Experiment', 'Cell line', 'Treatment', 'Time', 'Dose' exactly in this order.
path	A character indicating directory, where files with data are located.

Details

Example table structure (first argument) should look like this:

	Experiment	Cell line	Treatment	Time	Dose
array1.txt	Exp1	HCT116	C	0	0
array2.txt	Exp1	HCT116	C	0	0
array3.txt	Exp1	HCT116	IR	1	4
array4.txt	Exp1	HCT116	IR	2	4
array5.txt	Exp1	HCT116	IR	4	2

Note that in treatment column it shoul be C for control arrays and IR for treated ones (even if the samples were treated with for example chemicals and not with ionizing radiation).

If you have downloaded data from ArrayExpress database you can find information needed for creating above in .sdrf files.

This function is designed to load data for a single experiment. For loading many experiments at once you could use load_multi_miRNA.

Value

Function returns an object of uRNAList class.

See Also

load_multi_miRNA

Examples

## Not run: 
### this example shows how to load data downloaded from ArrayExpress database

# download data
datamiRNA = downloadAE('E-MTAB-5197', getwd())

# prepare table as shown in details, load it and make sure it's a character matrix
path_to_table = system.file("inst/extdata", "miRNA_ex1.rds", package = "FindReference")
my_table = readRDS(path_to_table)

# load data
loaded_data = load_miRNA(my_table, paste0(getwd(), 'E-MTAB-5197'))

## End(Not run)

EwaMarek/FindReference documentation built on May 30, 2019, 3:40 p.m.