Deconvolution of Tumour Profiles

Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.


News

ISOpureR 1.1.3 2019-05-10

Minor update

  • Removed stripping debug symbol table from binary output for CRAN compliance

ISOpureR 1.1.2 2018-05-01

Minor update

  • Fixing if() with conditions of length greater than one

ISOpureR 1.1.1 2018-01-10

Minor update

  • Shrunk down the test datafiles to save space, and fixed the Makevars to be compatible with Solaris

ISOpureR 1.1.0 2017-11-14

Major update

  • Added tac calculations
  • Fixing the bug noted by Francisco Avila Cobos which occurs when trying to run with only a single tumor

ISOpureR 1.0.21 2016-08-22

Minor update

  • Started importing graphicx for the vignette latex
  • Dropped the natwidth and natheight parameters in includegraphics call in the vignette latex

ISOpureR 1.0.19 2015-05-15

Minor update

  • changed email address
  • updated NEWS file

ISOpureR 1.0.18 2015-05-15

Minor update

  • added logging messages using futile.logger package
  • added some checks on the input tumour data (for zeros, minimum values, etc.) and if vv values are all 1

ISOpureR 1.0.17 2015-05-15

Minor update

  • changed one url address in vignette, so that it doesn't take as long to load

ISOpureR 1.0.16 2015-04-22

Minor update

  • edits to microarray example in vignette, so that now tumour and normal samples are normalized together, as they should be

ISOpureR 1.0.15 2015-03-31

Minor update

  • small edits to vignette
  • changed function names and corresponding .Rd files:
    • ISOpureS1.CPE.run.R to ISOpure.step1.CPE.R
    • ISOpureS2.PPE.run.R to ISOpure.step2.PPE.R

ISOpureR 1.0.14 2015-03-28

Minor update

  • changed function names and corresponding .Rd files:
    • ISOpureS1.model_core.learnmodel.R to ISOpureS1.CPE.run.R
    • ISOpureS2.model_core.learnmodel.R to ISOpureS2.PPE.run.R
  • corrected loop counter to run 35 not 34 times
  • updated data to match the data obtained after the updated loop

ISOpureR 1.0.13 2015-03-23

Minor update

  • made ajustements so that package will be less than 5 MB:
    • made figures in vignette folder with lower resolution
    • rounded the ISOpureS2model example data included in the package

ISOpureR 1.0.12 2015-03-19

Minor update

  • corrected vignette - make separate folder for figures that are generated within vignette

ISOpureR 1.0.11 2015-01-30

Minor update

  • include plotting of cellularity histogram, regular plot, and example heatmaps in vignette, using base R functions
  • update data: tumor and normal profiles to have probeset rownames and sample id colnames; include estimated alpha from full dataset; include probeset list
  • updated NEWS, had forgotten to add changes for version 1.0.10

ISOpureR 1.0.10 2015-02-06

Minor update

  • saved Bayesian network figure in Figures folder for vignette, as needed texlive/2012 to create it; it works in R with tools::texi2pdf

ISOpureR 1.0.9 2015-01-30

Minor update

  • for the vignette, added sections on the statistical model and on preprocessing of microarray data

ISOpureR 1.0.8 2015-01-07

Minor update

  • removed RcppEigen from the Imports field in the DESCRIPTION file, and added to LinkedTo field only
  • changed the data in inst/extdata/Beer to use a part of Beer data with 1000 transcripts, 30 patients in order to further decrease the memory use

ISOpureR 1.0.7 2014-12-18

Minor update

  • edited the .cpp file to use RcppEigen::Map which means the matrix is not copied, but accessed from the same memory location

ISOpureR 1.0.6 2014-12-16

Major update

  • used RcppEigen to create a C++ function wrapped into R that finds the maximum over columns, which improves run time 2-3 fold on the Beer dataset (both full and subset in package)
  • the package now depends on Rcpp and RcppEigen

ISOpureR 1.0.5 2014-11-20

Minor update

  • added NEWS file

bug fixes

  • DESCRIPTION FILE - updated date, was incorrect in previous version
  • changed the tests in inst/tests to use the updated data with 2500 transcripts, 43 patients
  • these tests are not really accessible to users, but are used to test the code in the vignette without having to run code in the vignette when loading (as it takes too long)

ISOpureR 1.0.4 2014-11-16

Minor update

  • changed the data in inst/extdata/Beer to use a part of Beer data with 2500 transcripts, 43 patients and ISOpureS2model was also rounded, in order to comply with CRAN memory requirements

Reference manual

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install.packages("ISOpureR")

1.1.3 by Paul C Boutros, 2 months ago


Browse source code at https://github.com/cran/ISOpureR


Authors: Gerald Quon [aut] , Catalina V Anghel [aut, trl] , Syed Haider [aut] , Francis Nguyen [aut] , Amit G Deshwar [aut] , Quaid D Morris [aut] , Paul C Boutros [aut, cre]


Documentation:   PDF Manual  


GPL-2 license


Imports Rcpp, stats, futile.logger

Suggests knitr

Linking to Rcpp, RcppEigen


Suggested by NNLM.


See at CRAN