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Streamlines descriptive analysis of quantitative mass spectrometry data.

Home Page: https://CRAN.R-project.org/package=quantable

R 100.00%

shiny report mass-spectrometry label-free-quantification cran quantitative-data

quantable's Introduction

protViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Documentation

The package ships with two pdf vignettes.

browseVignettes('protViz')

vignette('protViz')
vignette('PTM_MarkerFinder')

Installation

CRAN

install.packages('protViz')

from github

install the latest development version

install.packages('devtools')
library(devtools)
install_git('https://github.com/cpanse/protViz', build_vignettes = FALSE, quiet = FALSE)
library(protViz)

BiocManager::install('cpanse/protViz')

R CMD build hints

Rcpp::compileAttributes()

tools::package_native_routine_registration_skeleton(".", character_only = FALSE)


RcppExport SEXP _rcpp_module_boot_MyModule();

static const R_CallMethodDef CallEntries[] = {
    {"_rcpp_module_boot_MyModule", (DL_FUNC) &_rcpp_module_boot_MyModule, 0},
    {NULL, NULL, 0}
};

RcppExport void R_init_minModuleEx(DllInfo *dll) {
    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
    R_useDynamicSymbols(dll, FALSE);
}

Docker

docker pull cpanse/protviz \
&& docker run -d -p 8792:8787 cpanse/protviz

connect to http://yourdockerhost:8791 using a web browser

username: rstudio
password: rstudio

Documentation

The package ships with a package vignette (browseVignettes('protViz') and a reference manual (just type ?protViz on the R shell).

Both documents are also available on the package's CRAN page.

Related approaches

quantable's People

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jimhester lucaskook scottdaniel

quantable's Issues

determineCut - uses caret::confusionMatrix - check dependency

minimize dependenccies

Error: Unknown colour name: 4

I got the following error upon submission of pROC 1.16.0 to CRAN:

*** Changes to worse in reverse dependencies ***
Debian: <https://win-builder.r-project.org/incoming_pretest/pROC_1.16.0_20200112_115036/reverseDependencies/summary.txt>
 
Log dir: <https://win-builder.r-project.org/incoming_pretest/pROC_1.16.0_20200112_115036/>
The files will be removed after roughly 7 days.
 
Pretests:
Windows: <https://win-builder.r-project.org/incoming_pretest/pROC_1.16.0_20200112_115036/Windows/00check.log>
Debian: <https://win-builder.r-project.org/incoming_pretest/pROC_1.16.0_20200112_115036/Debian/00check.log>

[...]

Changes to worse in reverse depends:

Package: quantable
Check: examples
New result: ERROR
  Running examples in ‘quantable-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: addSpecialProteins
  > ### Title: add special labels
  > ### Aliases: addSpecialProteins
  > 
  > ### ** Examples
  > 
  > 
  > foldchange <- rnorm(1000)
  > pvals <-rexp(1000)
  > names <- sample(colors(),1000,replace=TRUE)
  > 
  > dataX <- data.frame(
  +   q.mod = pvals,
  +   log2FC = foldchange,
  +   names = names
  + )
  > library(rlang)
  > foldchange = "log2FC"
  > p <- volcano2GB(dataX, pthresh=0.1, log2FCThresh=0.5 , main='test',
  +                 repel.segment.size=0.3,
  +                 repel.text.size=2)
  > special <- sample(colors(),5)
  > p <- addSpecialProteins(p, dataX, special)
  > p
  Error: Unknown colour name: 4
  Execution halted

This was generated by CRAN's automatic checks of reverse dependencies and sent to me by email, temporarily blocking the submission of pROC 1.16.0.

As the error also happens on regular CRAN checks, I could ask CRAN to ignore it, and pROC 1.16.0 is now on CRAN. However it would be nice if you could fix it so it doesn't require manual intervention in the future.

Test simpleheatmap3 with missing values

heatmap3 fails when missing value. Develop strategy (i.e. remove rows) if this is the case.

Update documentation of robustscale

The function's default is TRUE but the documentation says FALSE
https://github.com/protViz/quantable/blob/master/R/robustscale.R

using factors in caret::confusionMatrix

The version of caret being sent to CRAN (6.0-79) has a change that affects your package. The details are here:

topepo/caret@e4dc43d

In summary, when creating a confusion matrix using two vectors, the input data are now required to be factors with the same levels. If this is an issue, you can get around it by creating a table and using confusionMatrix.table to get around the requirement.

The issues for your respective packages are shown below. When you submit to CRAN, please make sure that the dependency has caret (>= 6.0-79).

Let me know if you have any questions.

Thanks,

Max

    ...
    
    > ### Name: determineCut
    > ### Title: determine best Accuracy cuttoff
    > ### Aliases: determineCut
    > 
    > ### ** Examples
    > 
    > library(pROC)
    Type 'citation("pROC")' for a citation.
    
    Attaching package: ‘pROC’
    
    The following objects are masked from ‘package:stats’:
    
        cov, smooth, var
    
    > cases <- rnorm(100,-1,1.1)
    > controls <- rnorm(500,1,1.1)
    > cut <- determineCut(cases,controls)
    Error: `data` and `reference` should be factors with the same levels.
    Execution halted

protviz / quantable Goto Github PK

quantable's Introduction

protViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Documentation

Installation

CRAN

from github

R CMD build hints

Docker

Documentation

Related approaches

quantable's People

Contributors

Stargazers

Watchers

Forkers

quantable's Issues

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