Search
Question: minfi probe removal
0
gravatar for niutster
18 months ago by
niutster0
niutster0 wrote:

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

 

ADD COMMENTlink modified 18 months ago by James W. MacDonald47k • written 18 months ago by niutster0
0
gravatar for James W. MacDonald
18 months ago by
United States
James W. MacDonald47k wrote:

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,]
ADD COMMENTlink written 18 months ago by James W. MacDonald47k

Thanks, but minfi's objects are RGset or Methylset. There are not any eset.

ADD REPLYlink written 18 months ago by niutster0

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?

ADD REPLYlink written 18 months ago by James W. MacDonald47k

Thanks for your answer.

ADD REPLYlink written 18 months ago by niutster0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 252 users visited in the last hour