load_data: Loading microarray data from single experiment downloaded...

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

Description

load_data function loads data for a single microarray experiment downloaded from ArrayExpress database.

Usage

load_data(dane, ExpInfoTable, sdrfFile)

Arguments

dane	A list from downloadAE function.
platforma	Experiment's platform, could be 'Affymetrix' or 'Agilent'.
donotread	A character vector indicating which microarrays should not be loaded. Default is NA, which means that all microarrays listed in dane$rawFiles will be loaded.

Details

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

Note that only Agilent (one and double colour) and Affymetrix platforms are supported.

Loaded .sdrf file (second element of the output) could be useful for preparing table with experiment information needed for rep_elim or multi_rep_elim functions.

Value

Function returns a list with two elements. The first one is an object specific for array platform with raw expression data (could be marrayRaw or EListRaw for Agilent platform and AffyBatch or ExonFeatureSet for Affymetrix platform). The second element is a data frame with loaded .sdrf file.

See Also

load_multi_data

Examples

## Not run: 
### load all microarrays
dane = downloadAE("E-GEOD-21066", getwd())
loaded_experiment = load_data(dane, "Affymetrix")

### exclude some microarrays from loading
dane = downloadAE("E-GEOD-21066", getwd())
micrroarrays_under_conditions_imnot_interested = c("GSM526680.CEL", "GSM526756.CEL")
loaded_experiment = load_data(dane, "Affymetrix",
                         donotread = micrroarrays_under_conditions_imnot_interested)

### when you downloaded data with downloadAE
### but didn't assign the output into variable
downloadAE("E-GEOD-21066", getwd())

# read in data saved by downloadAE function
dane = readRDS('dataAE.rds')
loaded_experiment = load_data(dane, "Affymetrix")


## End(Not run)

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