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Implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer.

R 100.00%

cancer-data cancer-genomics cancer-research ovarian-cancer expression-database

consensusov's Introduction

Bioc-Release:

Bioc-Devel:

Overview

This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

Author: Gregory M Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Levi Waldron, Benjamin Haibe-Kains

Installation

# Installing the development version from GitHub:
# install.packages("devtools")
devtools::install_github("bhklab/consensusOV")

# Installing the release version from Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("consensusOV")

Usage

Extensive usage examples are provided in the consensusOV vignette on Bioconductor: consensusOV.pdf

Getting help

consensusov's People

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consensusov's Issues

Lists of signatures for subtypes

I've received a request for the lists of probesets Entrez IDs for the subtypes implemented in this package. I believe they're currently buried in compressed files of S4 objects; could you post them somewhere as plain text files that I can point interested readers to?

"uncompressed saves" warning -- data files have to be resaved

Data files have to be resaved (see below)

checking data for ASCII and uncompressed saves ... WARNING

Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
GSE14764.eset.RData 4.1Mb 3.6Mb xz
checking R/sysdata.rda ... NOTE

Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
sysdata.rda 7.3Mb 2.5Mb xz

ConcensusOV

Dears all,

I'm trying to apply consensusOV using RNAseq data and not microarray.
My data are TPM normalized.

Do you think that consensusOV could be applied to RNAseq data? Which normalization do you suggest ? Log2(TPM + 1) ?

Thank you for your help,

with best regards,

Laetitia Collet

LaTeX errors when creating PDF version

checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
You may want to clean up by 'rm -rf /tmp/RtmpQ4Krc6/Rd2pdf26776f63318d'

Repo out of sync with Bioc

Hi @gmchen @kofiav,

Can you please grant me push access to the Github repo?
I would like to initiate syncing the repo with Bioconductor and start to apply the discussed modifications.

Thanks!

Undocumented arguments warning

See below

checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'get.consensus.subtypes'
‘.dataset.names.to.keep’ ‘remove.using.cutoff’
‘percentage.dataset.removed’

Undocumented arguments in documentation object 'get.subtypes'
‘expression.dataset’ ‘...’
Documented arguments not in \usage in documentation object 'get.subtypes':
‘expression.matrix’

consensusOV

Dears all,

I have RNAseq raw count. Can you advise me the best normalization methods suitable to apply consensusOV.
VST or DESeq2’s median of ratios or EdgeR’s trimmed mean of M values (TMM) or TPM ?

Thank you in advance for your answer.

With best regards,

Laetitia Collet

bioccheck warning need to add unit tests

[1] "Consider adding unit tests. We strongly encourage them. See\n http://bioconductor.org/developers/how-to/unitTesting-guidelines/."

'MetaGx' import not declared

See error below:

checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘MetaGx’

sysdata branch

Hi @gmchen

I have merged the sysdata branch onto master.
Any additional developments that you are planning in this branch or can we delete it?

Method name conflict between Biobase and gdata

The following Warning is shown when R CMD check --no-build-vignettes consensusOV_1.0.tar.gz is executed. Both Biobase and gdata have methods called combine

checking whether package ‘consensusOV’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biobase::combine’ by ‘gdata::combine’ when loading ‘consensusOV’