This package was removed from CRAN on 2022-05-23. Its history is shown below.

Reason: check issues were not corrected despite reminders

Details below reflect version 1.0, its last release before removal.

mGSZ

1.0

Gene set analysis based on GSZ-scoring function and asymptotic p-value

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Pashupati Mishra1 releasesCRAN page ↗

Performs gene set analysis based on GSZ scoring function and asymptotic p-value. It is different from GSZ in that it implements asymptotic p-values instead of empirical p-values. Asymptotic p-values are calculated by fitting suitable distribution model to the null distribution. Unlike empirical p-values, resolution of asymptotic p-values are independent of the number of permutations and hence requires considerably fewer permutations. In addition, this package allows gene set analysis with seven other popular gene set analysis methods.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/mGSZ/mGSZ_1.0.tar.gz"
pkgFile <- "mGSZ_1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-mgsz

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 10%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

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Also on69 r2u239 bioconda

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (6)

R >= 3.0.0Biobase GSA limmaMASSismev

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,572 (72%)Rd 623 (28%)

Code characteristics

Cyclomatic complexity: 2.0 median / 20 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

40 0 exported

Complexity

3.2 avg / 20 max

Call network

40 nodes / 57 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Other (2)

Pashupati Mishra

Contributor

Petri Toronen

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-05-23
check issues were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
1.0
2014-02-19
R
R 3.0.0 released · 2013-04-03

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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