RPPASPACE

Description

Provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as 'tissue lysate arrays' or simply 'lysate arrays'. The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package named SuperCurve. For a detailed description of data inputs and outputs, usage information, and a list of related papers describing methods used in the package please review the vignette 'Guide_to_RPPASPACE'. 'RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data'. Bioinformatics Nov 15;38(22):5131-5133. <doi: 10.1093/bioinformatics/btac665>.

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CRAN Check Status

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

Error(s) in re-building vignettes:
--- re-building 'Guide_to_RPPASPACE.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `a1f5eada25eb960c163b7652f345b3cbdfe1eddb.png'
 not found: using draft setting.

Error: processing vignette 'Guide_to_RPPASPACE.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RPPASPACE.Rcheck/vign_test/RPPASPACE/vignettes/Guide_to_RPPASPACE.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Guide_to_RPPASPACE.log for more info.
--- failed re-building 'Guide_to_RPPASPACE.Rmd'

SUMMARY: processing the following file failed:
  'Guide_to_RPPASPACE.Rmd'

Error: Vignette re-building failed.
Execution halted

Check History

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

Error(s) in re-building vignettes:
--- re-building 'Guide_to_RPPASPACE.Rmd' using rmarkdown_notangle
! Package pdftex.def Error: File `a1f5eada25eb960c163b7652f345b3cbdfe1eddb.png'
 not found: using draft setting.

Error: processing vignette 'Guide_t
...[truncated]...
/#debugging for debugging tips. See Guide_to_RPPASPACE.log for more info.
--- failed re-building 'Guide_to_RPPASPACE.Rmd'

SUMMARY: processing the following file failed:
  'Guide_to_RPPASPACE.Rmd'

Error: Vignette re-building failed.
Execution halted

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’
  All declared Imports should be used.

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