Newbie question: how do I address a subset obtained by split()?
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@yuliachupalova-17234
Last seen 3.1 years ago

Hi,
Extreme newbie question: I need to calculate stats for a subset of a flowSet generated by split(). The subset is reported as follows: 

$`area 2`
A flowSet with 1 experiments.
An object of class 'AnnotatedDataFrame' ...

I cannot figure out how to use this subset - what is the syntax to address it? I've tried:

> $`area 2`
Error: unexpected '$' in "$"
> `area 2`
Error: object 'area 2' not found
> singlets$`area 2`
NULL

Below is how I arrived at the split, if that matters. 
Thanks!

---------------------------------------

> fset <- read.flowSet("x.fcs")
> tf <- transformList(from=colnames(fset)[5:30], tfun=asinh)
> fset_t <- tf %on% fset
> beadgate <- norm2Filter("SSC-A", "FSC-A")
> singletgate <- norm2Filter("FSC-A", "FSC-H")
> beads <- Subset(fset_t, beadgate)
> singlets <- Subset(beads, singletgate)
> c2f <- curv2Filter(x=list("FL1-A", "FL3-A"), bwFac=0.4)
> peaks <- filter(singlets, c2f)
> summary(peaks)
filter summary for frame 'x.fcs'
 rest: 115 of 1656 events (6.94%)
 area 1: 97 of 1656 events (5.86%)
 area 2: 179 of 1656 events (10.81%)
 area 3: 196 of 1656 events (11.84%)
 area 4: 218 of 1656 events (13.16%)
 area 5: 221 of 1656 events (13.35%)
 area 6: 177 of 1656 events (10.69%)
 area 7: 227 of 1656 events (13.71%)
 area 8: 199 of 1656 events (12.02%)
 area 9: 27 of 1656 events (1.63%)

> split(singlets, peaks)
$`rest`
A flowSet with 1 experiments.

An object of class 'AnnotatedDataFrame'
  rowNames: x.fcs
  varLabels: name population
  varMetadata: labelDescription

  column names:
  FSC-H FSC-A SSC-H SSC-A FL1-H FL1-A FL2-H FL2-A FL3-H FL3-A FL4-H FL4-A FL5-H FL5-A FL6-H FL6-A FL7-H FL7-A FL8-H FL8-A FL9-H FL9-A FL10-H FL10-A FL11-H FL11-A FL12-H FL12-A FL13-H FL13-A FSC-Width Time

$`area 1`
A flowSet with 1 experiments.

An object of class 'AnnotatedDataFrame'
  rowNames: x.fcs
  varLabels: name population
  varMetadata: labelDescription

  column names:
  FSC-H FSC-A SSC-H SSC-A FL1-H FL1-A FL2-H FL2-A FL3-H FL3-A FL4-H FL4-A FL5-H FL5-A FL6-H FL6-A FL7-H FL7-A FL8-H FL8-A FL9-H FL9-A FL10-H FL10-A FL11-H FL11-A FL12-H FL12-A FL13-H FL13-A FSC-Width Time

$`area 2`
A flowSet with 1 experiments.

An object of class 'AnnotatedDataFrame'
  rowNames: x.fcs
  varLabels: name population
  varMetadata: labelDescription

  column names:
  FSC-H FSC-A SSC-H SSC-A FL1-H FL1-A FL2-H FL2-A FL3-H FL3-A FL4-H FL4-A FL5-H FL5-A FL6-H FL6-A FL7-H FL7-A FL8-H FL8-A FL9-H FL9-A FL10-H FL10-A FL11-H FL11-A FL12-H FL12-A FL13-H FL13-A FSC-Width Time

$`area 3` ...

flowStats newbie split subset flowCore • 465 views
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Entering edit mode

You have to store the result in a variable, then you can access it.

res.split <- split(singlets, peaks)
res.split$`area 2`
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THANKS so much!!!

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