minfi probe removal
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niutster • 0
@niutster-10602
Last seen 6.4 years ago

Hi,

I am using minfi to pre-processes methylation files but i don't know how can I remove probes with a certain p-value, there is not any command in tutorial to tell me about it.

Thanks

 

minfi probe • 1.8k views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

All of the objects used in the minfi package inherit from either the eSet or RangedSummarizedExperiment class, so they act identically to a data.frame under subsetting. In other words if you have your data in an object called, say, 'eset', and you have a vector of p-values (called 'pval') with the same length as nrow(eset), then you can do

c <- {some value goes here}
filtered.eset <- eset[pval < c,]
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Thanks, but minfi's objects are RGset or Methylset. There are not any eset.

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Really? Are you sure about that? Let's check...

> getClass("MethylSet")
Class "MethylSet" [package "minfi"]

Slots:
                                                               
Name:    preprocessMethod          assayData          phenoData
Class:          character          AssayData AnnotatedDataFrame
                                                               
Name:         featureData     experimentData         annotation
Class: AnnotatedDataFrame              MIAxE          character
                                            
Name:        protocolData  .__classVersion__
Class: AnnotatedDataFrame           Versions

Extends:
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
> getClass("RGChannelSet")
Class "RGChannelSet" [package "minfi"]

Slots:
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:      experimentData         annotation       protocolData
Class:              MIAxE          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

Extends:
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3

Known Subclasses: "RGChannelSetExtended"
> getClass("GenomicRatioSet")
Class "GenomicRatioSet" [package "minfi"]

Slots:
                                                            
Name:            preprocessMethod                 annotation
Class:                  character                  character
                                                            
Name:                   rowRanges                    colData
Class: GenomicRangesORGRangesList                  DataFrame
                                                            
Name:                      assays                      NAMES
Class:                     Assays            characterORNULL
                                                            
Name:             elementMetadata                   metadata
Class:                  DataFrame                       list

Extends:
Class "RangedSummarizedExperiment", directly
Class "SummarizedExperiment", by class "RangedSummarizedExperiment", distance 2
Class "Vector", by class "RangedSummarizedExperiment", distance 3
Class "Annotated", by class "RangedSummarizedExperiment", distance 4

That said, what's your point? Was my answer unhelpful? Why are you arguing about something you seem to be ignorant of?

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Thanks for your answer.

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