get parameters of estimateLogicle
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Guest User ★ 12k
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Last seen 8.4 years ago
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")) > str(lgcl) Formal class 'transformList' [package "flowCore"] with 2 slots ..@ transforms :List of 2 .. ..$ FL3-H:Formal class 'transformMap' [package "flowCore"] with 3 slots .. .. .. ..@ output: chr "FL3-H" .. .. .. ..@ input : chr "FL3-H" .. .. .. ..@ f :function (x) .. ..$ FL4-H:Formal class 'transformMap' [package "flowCore"] with 3 slots .. .. .. ..@ output: chr "FL4-H" .. .. .. ..@ input : chr "FL4-H" .. .. .. ..@ f :function (x) ..@ transformationId: chr "defaultTransformation" > > lgcl <- logicleTransform(w = 0.74, t=2^18, m =4.5) > str(lgcl) Formal class 'transform' [package "flowCore"] with 2 slots ..@ transformationId: chr "defaultLogicleTransform" ..@ .Data :function (x) > summary(lgcl) $a [1] 0 $k transform object 'defaultLogicleTransform' $m [1] 4.5 $t [1] 262144 $transformationId [1] "defaultLogicleTransform" $w [1] 0.74 -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 16 months ago
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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@transforms,function(transMap) summary(new("transform", .Data = transMap@f)) ,simplify =FALSE) }) | and then |summary(lgcl)| Mike On 02/26/2014 03:00 AM, bioconductor-request@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 [[alternative HTML version deleted]]
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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
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