[BioC] Subsetting data from RGList (Again)

[Martin Morgan]

Getting a little carried away there, it's just

> idx <- match(a$Gene.Probe, R$genes$ProbeName)

without the 'which'

Martin

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Hi Elliott,
>
> "elliott harrison" <e.harrison at epistem.co.uk> writes:
>
>> Hi All, 
>> Sorry to trouble everyone  but I didn't get my subsetting of an RGList
>> sorted last week.
>> I've tried loads of different combinations of things that were suggested
>> but not quite there yet.
>>
>> MY Data is an RGList object here is a bit
> [SNIP]
>> $genes
>>   Row Col FeatureNum ProbeUID ControlType       ProbeName
>> GeneName  SystematicName   Status
>> 1   1   1          1        0           1 GE_BrightCorner
>> GE_BrightCorner GE_BrightCorner Control6
>>  
>> $source
>> [1] "generic"
>>  
>>  
>> My list of probes to select data with is in this object.
>>> a
>>            Gene.Probe
>> Probe1   A_24_P329635
>> Probe2   A_23_P104098
>> Probe3   A_23_P419038
>> Probe4   A_24_P124550
>> Probe5    A_23_P99044
>   
> You'd like to match your 'Gene.Probe' column, I guess, to a column in
> R$genes, maybe ProbeName? So create a numeric vector, with the
> locations of each Gene.Probe in R$Genes$ProbeName
>
>> idx <- which(match(a$Gene.Probe, R$genes$ProbeName))
>
> and use it to subset R
>
>> R[idx,]
>
> If you'd wanted to match Probe1, etc, you'd have used rownames(a)
> instead of a$Gene.Probe. Sometimes RGList has row names, i.e.,
>
>> rownames(R)
>
> returns a (long!) character vector. In these cases, you can create a
> character vector 'rnms' containing at least some of the row names of
> R. and
>
>> R[rnms,]
>
> Martin
>
>>  
>>  
>> I've tried
>> A=rownames(a)
>> RA = R[A,]
>>  
>> But don't get any genes
>>>$genes
>> [1] Row            Col            FeatureNum     ProbeUID
>> ControlType    ProbeName      GeneName       SystematicName Status
>>
>> <0 rows> (or 0-length row.names)
>>  
>> I've tried creating a vector using match a load of different ways but it
>> is always empty
>>>vec = match(A, R)
>>>vec = match(A, R$genes$ProbeName)
>>>vec = match(A, R$genes)
>>>vec = match(probelist600, R)
>>>vec = match(probelist600, R$genes)
>>>vec = match(probelist600, R$genes$ProbeName)
>>  
>>  
>> This is part what ends up in object A
>>> A
>>   [1] "Probe1"   "Probe2"   "Probe3"   "Probe4"   "Probe5"   "Probe6"
>> "Probe7"   "Probe8"   "Probe9"   "Probe10"  "Probe11"  "Probe12"
>> "Probe13" 
>>
>> I expected to see my probe names in there.
>> I'm clearly not getting something. 
>> Can anyone see where I'm going wrong?
>> Many Thanks
>> Elliott
>>
>>
>> This message has been scanned for viruses by BlackSpider...{{dropped:3}}
>>
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>
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