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% Generated by roxygen2 (4.1.1): do not edit by hand |
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% Please edit documentation in R/cleanMetadata.GSE10846.R, R/cleanMetadata.GSE11318.R, R/cleanMetadata.GSE31312.R, R/cleanMetadata.GSE34171.R, R/cleanMetadata.GSE56315.R, R/cleanMetadata.R |
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\name{cleanMetadata.GSE10846} |
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\alias{cleanMetadata} |
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\alias{cleanMetadata.GSE10846} |
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\alias{cleanMetadata.GSE11318} |
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\alias{cleanMetadata.GSE31312} |
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\alias{cleanMetadata.GSE34171} |
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\alias{cleanMetadata.GSE56315} |
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\alias{cleanMetadata.data.frame} |
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\title{Generic metadata cleaning function} |
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\usage{ |
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\method{cleanMetadata}{GSE10846}(meta_data) |
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\method{cleanMetadata}{GSE11318}(meta_data) |
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\method{cleanMetadata}{GSE31312}(meta_data) |
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\method{cleanMetadata}{GSE34171}(meta_data) |
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\method{cleanMetadata}{GSE56315}(meta_data) |
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cleanMetadata(meta_data) |
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\method{cleanMetadata}{data.frame}(meta_data) |
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} |
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\arguments{ |
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\item{meta_data}{Output from \code{downloadAndPrepareMetadata}.} |
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} |
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\value{ |
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Returns a specifically cleaned \code{data.frame} for the GEO dataset. |
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} |
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\description{ |
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S3 method dispatch giving the custom functions for formatting datasets. |
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The function \code{downloadAndPrepareMetadata} adds a class \code{"GSEXXXX"} |
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of the GEO number in question. |
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The generic looks for functions of the name \code{cleanMetadata.GSEXXXX} and |
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specific for that dataset and cleans metadata using that function. |
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} |
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\details{ |
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GSE10846:\cr |
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The cleanup of GSE10846 (LLMPP) adds two batches corresponding to each |
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the CHOP and the R-CHOP cohort. |
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GSE11318:\cr |
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The cleanup of GSE11318 (NCI) adds the batch corresponding to |
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platform GPL570 (HG-U133 plus 2) and excludes the GPL6400 samples. |
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GSE31312:\cr |
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This function makes the samples GSM776068, GSM776149, and GSM776462 to be |
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left out of the downstream preprocessing due to bad array quality. |
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GSE34171:\cr |
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The cleanup of GSE34171 (MDFCI) adds three batches corresponding to each |
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platform (HG-U133 plus 2, HG-U133A, HG-U133B). |
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GSE56315:\cr |
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The cleanup of GSE56315 (CHEPRETRO) adds two batches corresponding to each |
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clinical samples and normal sorted tissues both on platform |
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HG-U133 plus 2. |
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} |
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\author{ |
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Anders Ellern Bilgrau, Steffen Falgreen Larsen |
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} |
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