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
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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version 2.3.6
Thanks, but minfi's objects are RGset or Methylset. There are not any eset.
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 4That said, what's your point? Was my answer unhelpful? Why are you arguing about something you seem to be ignorant of?
Thanks for your answer.