[BioC] flowCore - how to see the marker names?

[Nolwenn LeMeur]

Hi Anne,

The parameter annotation of a flowframe is stored in an annotated 
dataframe. You can access the information using the pData function:

pData(parameters(FCS))


see the flowFrame-class  man page for more details

Nolwenn

Anne wrote:

>Hi,
> 
>I am having problems in finding the marker names in a flowFrame. 
>(The marker names mapped onto the channel names - i.e.FL1-H, FL2-H, FL3-H
>and FL4-H). 
> 
>I wrote the code:
> 
>FCS <- read.FCS(subfilesdir2)
>FCS 
>featureNames(FCS)
> 
>and got this output - but it does not seem to show any new names (i.e CD45),
>so am I doing the right thing:
>
>flowFrame object 'P:/Projekter/Scientific Projects/AML_subgroup specific
>gene expression_2008/Part A/Data/Raa
>data/AML_FC_Herlev/de39patienter/BH13100/BH13100.002'
>with 100000 cells and 7 observables:
>     name       desc range minRange maxRange
>$P1 FSC-H FSC-Height  1024        0     1023
>$P2 SSC-H SSC-Height  1024        0     1023
>$P3 FL1-H FL1-Height  1024        1    10000
>$P4 FL2-H FL2-Height  1024        1    10000
>$P5 FL3-H FL3-Height  1024        1    10000
>$P6 FL1-A       <NA>  1024        0     1023
>$P7 FL4-H FL4-Height  1024        1    10000
>132 keywords are stored in the 'descripton' slot
>  
>
>>featureNames(FCS)
>>    
>>
>   $P1N    $P2N    $P3N    $P4N    $P5N    $P6N    $P7N 
>"FSC-H" "SSC-H" "FL1-H" "FL2-H" "FL3-H" "FL1-A" "FL4-H" 
>
>Thanks in advance
> 
>/Anne
> 
>
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