load_multi_data: Loading microarray data from a list of experiments downloaded...

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

Description

load_multi_data function loads data for a list of microarray experiments downloaded from ArrayExpress database.

Usage

load_multi_data(dane, ExpInfoTable, sdrfFiles)

Arguments

dane	A list of lists from downloadAE function.
platforma	A character vector indicating platform for each experiment. Supported platforms are 'Affymetrix' and 'Agilent'.
donotread	A list of character vectors indicating which microarrays should not be loaded for each experiment. Default is NA, which means that all microarrays listed in dane$rawFiles will be loaded. Note that list's length must be the same as the length of list 'dane'.

Details

This function is designed to read in microarray data from many experiments. For more detail see load_data function help.

Value

Function returns a list with two elements. The first one is a list of objects specific for array platform with raw expression data. The second element is a list of data frames with loaded .sdrf files for each experiment.

See Also

load_data

Examples

## Not run: 
### load all microarrays for two experiments
to_download = c("E-GEOD-21066", "E-MTAB-966")
platforms = c("Affymetrix", "Agilent")

dane = downloadAE(to_download, getwd())
loaded_experiments = load_multi_data(dane, platforms)

### do not load some microarrays from the first experiment
to_download = c("E-GEOD-21066", "E-MTAB-966")
platforms = c("Affymetrix", "Agilent")

dane = downloadAE(to_download, getwd())

# for second experiment all microarrays should be loaded
# -> the second element of the list is NA
unwanted_arrays = list(c("GSM526680.CEL", "GSM526756.CEL"), NA)

# or (which could be useful when there are a lot of experiments)
unwanted_arrays = rep(list(list(NA)), length(dane))
unwanted_arrays[[1]] = c("GSM526680.CEL", "GSM526756.CEL")

loaded_experiment = load_multi_data(dane, platforms, donotread = unwanted_arrays)

### when you downloaded data with downloadAE
### but didn't assign the output into variable

to_download = c("E-GEOD-21066", "E-MTAB-966")
platforms = c("Affymetrix", "Agilent")
downloadAE(to_download, getwd())

# read in data saved by downloadAE function
dane = readRDS('dataAE.rds')
loaded_experiment = load__multi_data(dane, platforms)


## End(Not run)

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