summarizeSensitivityProfiles not working, similar to issue#124

[cicGuoH]

sorry, I'm new. Content is below.

[cicGuoH]

Hello, I was trying to use function summarizeSensitivityProfiles and I got this error similar to #124 . I followed the suggestions below that I first downloaded the PSet, however, error is still here. Here is my code.

# CCLE <- downloadPSet("CCLE_2015", saveDir = "../Data/PharmacoGx")
CCLE <- readRDS("../Data/PharmacoGx/CCLE_2015.rds")
ccle.acc <- PharmacoGx::summarizeSensitivityProfiles(
  pSet=CCLE,
  sensitivity.measure='aac_recomputed',
  verbose=TRUE)

The error information is:

Error in (function (classes, fdef, mtable)  : 
  函数‘summarizeSensitivityProfiles’标签‘"missing"’找不到继承方法

I think its version in english is

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘summarizeSensitivityProfiles’ for signature ‘"missing"’

And the demo example data(CCLEsmall) can work well.

[ChristopherEeles]

Hi @cicGuoH,

The argument name for passing a PharmacoSet into many of our functions has changed from pSet to object. This allows us to reuse these methods in other packages such as ToxicoGx and RadioGx, which have their own respective classes (ToxicoSet and RadioSet).

Our documentation has been updated to reflect these changes: https://bioconductor.org/packages/devel/bioc/vignettes/PharmacoGx/inst/doc/PharmacoGx.html. Perhaps you are following an old tutorial?

Either way, this should work:

ccle.acc <- PharmacoGx::summarizeSensitivityProfiles(
  object=CCLE,
  sensitivity.measure='aac_recomputed',
  verbose=TRUE)

If you still get the error, please try printing out your PharmacoSet variable to make sure it loaded correctly.

Best, Christopher Eeles Software Developer Haibe-Kains Lab PMCC | UHN

[cicGuoH]

Thank you very much. I changed from PSet into object and it works. Sorry for my carelessness.