[BioC] get parameters of estimateLogicle

[Samuel GRANJEAUD IR/INSERM]

Perfect as usual.

Thanks,
Samuel

> object = lgcl
> sapply(object at transforms, function(transMap) summary(new("transform", 
> .Data = transMap at f))  ,simplify = FALSE)
$`FL3-H`
$`FL3-H`$a
[1] 0

$`FL3-H`$k
transform object 'FL3-H_logicleTransform'

$`FL3-H`$m
[1] 4.5

$`FL3-H`$t
[1] 10000

$`FL3-H`$transformationId
[1] "FL3-H_logicleTransform"

$`FL3-H`$w
[1] 0


$`FL4-H`
$`FL4-H`$a
[1] 0

$`FL4-H`$k
transform object 'FL4-H_logicleTransform'

$`FL4-H`$m
[1] 4.5

$`FL4-H`$t
[1] 10000

$`FL4-H`$transformationId
[1] "FL4-H_logicleTransform"

$`FL4-H`$w
[1] 0




On 26-02-2014 20:07, Mike wrote:
> There isn't such function available for transformList. but you can
> write something like this:
> 
>  setMethod("summary",
>  signature=signature(object="transformList"),
>  definition=function(object, ...)
>  {
>  sapply(object at transforms, function(transMap)
>  summary(new("transform", .Data = transMap at f))
>  ,simplify = FALSE)
>  })
> 
> and then summary(lgcl)
> 
> Mike
> 
> On 02/26/2014 03:00 AM, bioconductor-request at r-project.org wrote:
> 
>> Hi,
>> 
>> I would to get the parameters a, w, m, t that the estimateLogicle
>> computes. The question may be extended to how to get parameters from
>> a transformList or a transformMap. What I would like, is a function
>> that returns the same information as summary applied to a user
>> defined transform.
>> 
>> Cheers.
>> 
>>>> data(GvHD)
>>>> samp <- GvHD[[1]]
>>>> lgcl <- estimateLogicle(samp, channels = c("FL3-H", "FL4-H"))
>>>> lgcl <- logicleTransform(w = 0.74, t=2^18, m =4.5)
>>>> summary(lgcl)
>> 
>> $a
>> [1] 0
>> 
>> $k
>> transform object 'defaultLogicleTransform'
>> 
>> $m
>> [1] 4.5
>> 
>> $t
>> [1] 262144
>> 
>> $transformationId
>> [1] "defaultLogicleTransform"
>> 
>> $w
>> [1] 0.74