cleanMetadata: Generic metadata cleaning function

In AEBilgrau/DLBCLdata: Automated and reproducible download and preprocessing of DLBCL data

Description

S3 method dispatch giving the custom functions for formatting datasets. The function downloadAndPrepareMetadata adds a class "GSEXXXX" of the GEO number in question. The generic looks for functions of the name cleanMetadata.GSEXXXX and specific for that dataset and cleans metadata using that function.

Usage

## S3 method for class 'GSE10846'
cleanMetadata(meta_data)

## S3 method for class 'GSE11318'
cleanMetadata(meta_data)

## S3 method for class 'GSE31312'
cleanMetadata(meta_data)

## S3 method for class 'GSE34171'
cleanMetadata(meta_data)

## S3 method for class 'GSE56315'
cleanMetadata(meta_data)

cleanMetadata(meta_data)

## S3 method for class 'data.frame'
cleanMetadata(meta_data)

Arguments

meta_data

Output from downloadAndPrepareMetadata.

Details

GSE10846:
The cleanup of GSE10846 (LLMPP) adds two batches corresponding to each the CHOP and the R-CHOP cohort.

GSE11318:
The cleanup of GSE11318 (NCI) adds the batch corresponding to platform GPL570 (HG-U133 plus 2) and excludes the GPL6400 samples.

GSE31312:
This function makes the samples GSM776068, GSM776149, and GSM776462 to be left out of the downstream preprocessing due to bad array quality.

GSE34171:
The cleanup of GSE34171 (MDFCI) adds three batches corresponding to each platform (HG-U133 plus 2, HG-U133A, HG-U133B).

GSE56315:
The cleanup of GSE56315 (CHEPRETRO) adds two batches corresponding to each clinical samples and normal sorted tissues both on platform HG-U133 plus 2.

Value

Returns a specifically cleaned data.frame for the GEO dataset.

Author(s)

Anders Ellern Bilgrau, Steffen Falgreen Larsen

AEBilgrau/DLBCLdata documentation built on May 5, 2019, 11:29 a.m.