champ.load getting filtered RGChannelSet
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hrishi27n ▴ 20
@hrishi27n-11821
Last seen 12 weeks ago
United States

Hello,

I am using champ.load to filter my probes from my IDAT files. I understand the champ.load function returns mset,rgset,pd,beta etc. I see that the mset includes the filtered features(everything left after det P,dropSNP,dropXY), but the rgset is unchanged, I have pasted a section of the output below.

For what I am trying to do, I need a filtered rgset, is there a way to get this? 

 

myLoad$rgSet

RGChannelSetExtended (storageMode: lockedEnvironment)

assayData: 622399 features, 85 samples 

  element names: Green, GreenSD, NBeads, Red, RedSD 

An object of class 'AnnotatedDataFrame'

  sampleNames: 4640959416005296128 6658290574090567680 ...

    5865657039673360384 (85 total)

  varLabels: Sample_Name Sample_Well ... filenames (13 total)

  varMetadata: labelDescription

Annotation

  array: IlluminaHumanMethylation450k

  annotation: ilmn12.hg19

> myLoad$mset

MethylSet (storageMode: lockedEnvironment)

assayData: 434663 features, 85 samples 

  element names: Meth, Unmeth 

An object of class 'AnnotatedDataFrame'

  sampleNames: 4640959416005296128 6658290574090567680 ...

    5865657039673360384 (85 total)

  varLabels: Sample_Name Sample_Well ... filenames (13 total)

  varMetadata: labelDescription

Annotation

  array: IlluminaHumanMethylation450k

  annotation: ilmn12.hg19

Preprocessing

  Method: Raw (no normalization or bg correction)

  minfi version: 1.20.0

  Manifest version: 0.4.0

 

champ methylation • 671 views
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Entering edit mode
Yuan Tian ▴ 90
@yuan-tian-9598
Last seen 22 months ago

Hello:

 

Sorry I just see this. Based on current version of ChAMP, it can not do filtering on rgSet data. I am not sure if minfi provide. I will check if I can code that out and add this feature in future version of ChAMP.

 

Best

Yuan Tian

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