ICBioMark

Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers

v0.1.4 · Nov 15, 2021 · MIT + file LICENSE

Description

Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) <arXiv:2102.04296>. This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	62.5s
r-devel-linux-x86_64-debian-gcc	NOTE	48.3s
r-devel-linux-x86_64-fedora-clang	NOTE	100s
r-devel-linux-x86_64-fedora-gcc	NOTE	85.4s
r-devel-macos-arm64	NOTE	19s
r-devel-windows-x86_64	NOTE	86s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	58s
r-oldrel-windows-x86_64	NOTE	111s
r-patched-linux-x86_64	NOTE	57.9s
r-release-linux-x86_64	NOTE	56.2s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	70s
r-release-windows-x86_64	NOTE	91s

Check details (16 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Jacob R. Bradley <cobrbradley@gmail.com>’

The Description field contains
  and Cannings (2021) <arXiv:2102.04296>. This package allows the user to
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Jacob R. Bradley <cobrbradley@gmail.com>’

The Description field contains
  and Cannings (2021) <arXiv:2102.04296>. This package allows the user to
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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NOTE r-devel-linux-x86_64-fedora-gcc

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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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NOTE r-devel-macos-arm64

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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-windows-x86_64

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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-patched-linux-x86_64

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checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Jacob R. Bradley <cobrbradley@gmail.com>’

The Description field contains
  and Cannings (2021) <arXiv:2102.04296>. This package allows the user to
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Jacob R. Bradley <cobrbradley@gmail.com>’

The Description field contains
  and Cannings (2021) <arXiv:2102.04296>. This package allows the user to
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
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    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

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Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

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Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                     ^
checkRd: (-1) get_p.Rd:29: Lost braces; missing escapes or markup?
    29 | \item A numeric p_norm, giving the factor between p_{gs} and phi_{0gs} (see paper for details).
       |                                                                  ^

Dependency Network

Version History

new 0.1.4 Mar 9, 2026

Maintainer

Jacob R. Bradley

Dependencies

Depends

R (>= 2.10)

Imports

stats utils glmnet Matrix dplyr purrr latex2exp matrixStats ggplot2 gglasso PRROC

Suggests

testthat (>= 2.1.0)

Compilation

No compilation needed

First Published

Mar 9, 2026

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