norm_and_annot_miRNA: Normalization and annotation of microarray miRNA data

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

Description

norm_and_annot_miRNA function loads normalizes and annotates data from miRNA microarray experiments performed on Agilent platform.

Usage

norm_and_annot_miRNA(loaded_data)

Arguments

loaded_data

An object of class uRNAList or a list of objects of this type.

Details

Data are rma background corrected and normalized. They are annotated with MIMAT ids.

Value

Function returns an expression matrix (or list of them if argument was a list) with normalized and annotated expression values.

Examples

## Not run: 
### download data from ArrayExpress database
AEids = c("E-MTAB-5197", "E-GEOD-59862")
datamiRNA = downloadAE(AEids, getwd())

### prepare tables as shown in details, load them and make sure they're character matrices
path_to_tables = system.file("inst/extdata", "miRNA_ex2.rds", package = "FindReference")
my_tables = readRDS(path_to_tables)

### load data

# for data downloaded from ArrayExpress you can easily get the second argument by:
all_paths = sapply(datamiRNA, function(x){x$path})

loaded_data = load_multi_miRNA(my_tables, all_paths)

### normalize and annotate data
norm_data = norm_and_annot_miRNA(loaded_data)

## End(Not run)

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