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PSCBS

🔬 R package: Analysis of Parent-Specific DNA Copy Numbers

https://github.com/henrikbengtsson/pscbs

Science Score: 36.0%

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package r

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affymetrix copy-number dna expression large-scale microarray notebook reproducibility rna
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🔬 R package: Analysis of Parent-Specific DNA Copy Numbers

Basic Info
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  • Stars: 7
  • Watchers: 4
  • Forks: 4
  • Open Issues: 11
  • Releases: 0
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package r
Created over 11 years ago · Last pushed about 2 years ago
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Readme Changelog Contributing

README.md

CRAN check status R CMD check status Top reverse-dependency checks status

PSCBS: Analysis of Parent-Specific DNA Copy Numbers

The PSCBS package implements the parent-specific copy-number segmentation presented in Olshen et al. (2011). Package vignette 'Parent-specific copy-number segmentation using Paired PSCBS' provides a detailed introduction for running PSCBS segmentation. It's available as:

r vignette("PairedPSCBS", package = "PSCBS")

Below is an excerpt of the example found in that vignette:

```r library(PSCBS)

Get single-chromosome example data

data <- exampleData("paired.chr01") str(data)

’data.frame’: 73346 obs. of 6 variables:

$ chromosome: int 1 1 1 1 1 1 1 1 1 1 ...

$ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127..

$ CT : num 1.625 1.071 1.406 1.18 0.856 ...

$ betaT : num 0.757 0.771 0.834 0.778 0.229 ...

$ CN : num 2.36 2.13 2.59 1.93 1.71 ...

$ betaN : num 0.827 0.875 0.887 0.884 0.103 ...

Drop total copy-number outliers

data <- dropSegmentationOutliers(data)

Identify chromosome arms from data

gaps <- findLargeGaps(data, minLength = 1e+06) knownSegments <- gapsToSegments(gaps)

Parent-specific copy-number segmentation

fit <- segmentByPairedPSCBS(data, knownSegments = knownSegments)

Get segments as a data.frame

segments <- getSegments(fit, simplify = TRUE) segments

chromosome tcnId dhId start end tcnNbrOfLoci tcnMean

1 1 1 1 554484 33414619 9413 1.381375

2 1 1 2 33414619 86993745 17433 1.378570

3 1 2 1 86993745 87005243 2 3.185100

4 1 3 1 87005243 119796080 10404 1.389763

5 1 3 2 119796080 119932126 72 1.470789

6 1 3 3 119932126 120992603 171 1.439620

7 1 4 1 120992604 141510002 0 NA

8 1 5 1 141510003 185527989 13434 2.065400

9 1 6 1 185527989 199122066 4018 2.707400

10 1 7 1 199122066 206512702 2755 2.586100

11 1 8 1 206512702 206521352 14 3.871900

12 1 9 1 206521352 247165315 15581 2.637500

tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean

1 2765 2765 2765 0.4868 0.3544608 1.0269140

2 4544 4544 4544 0.5185 0.3318907 1.0466792

3 0 0 0 NA NA NA

4 2777 2777 2777 0.5203 0.3333347 1.0564285

5 8 8 8 0.0767 0.6789900 0.7917995

6 52 52 52 0.5123 0.3510514 1.0885688

7 0 0 NA NA NA NA

8 3770 3770 3770 0.0943 0.9353164 1.1300836

9 1271 1271 1271 0.2563 1.0067467 1.7006533

10 784 784 784 0.2197 1.0089669 1.5771331

11 9 9 9 0.2769 1.3998854 2.4720146

12 4492 4492 4492 0.2290 1.0167563 1.6207438

Plot copy-number tracks

plotTracks(fit) ```

Parallel processing

The package supports segmentation of the chromosomes in parallel (asynchronously) via futures by adding the following

r future::plan("multisession")

to the beginning of the PSCBS script. Everything else will work the same. To reset to non-parallel processing, use future::plan("sequential").

To configure this automatically whenever the package is loaded, see future vignette 'A Future for R: Controlling Default Future Strategy'.

References

  • Bengtsson H, Neuvial P, Speed TP. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010. DOI: 10.1186/1471-2105-11-245. PMID: 20462408, PMCID: PMC2894037

  • Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VA. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011. DOI: 10.1093/bioinformatics/btr329. PMID: 21666266. PMCID: PMC3137217

Installation

R package PSCBS is available on CRAN and can be installed in R as:

```r

install.packages("BiocManager")

BiocManager::install(c("aroma.light", "DNAcopy"))

install.packages("PSCBS") ```

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

r remotes::install_github("HenrikBengtsson/PSCBS", ref="develop")

This will install the package from source.

Owner

  • Name: Henrik Bengtsson
  • Login: HenrikBengtsson
  • Kind: user
  • Company: UCSF

Assoc Professor. R Foundation. R Consortium. Many R packages, e.g. future & matrixStats.

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Last synced: over 2 years ago

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  • Total Commits: 754
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  • Avg Commits per committer: 188.5
  • Development Distribution Score (DDS): 0.009
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  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Henrik Bengtsson hb@a****g 747
gara-z g****a@g****m 5
Adam Olshen o****n@y****m 1
Pierre Neuvial p****l@g****r 1
Committer Domains (Top 20 + Academic)
genopole.cnrs.fr: 1 aroma-project.org: 1

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Last synced: 11 months ago

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  • Total issues: 64
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Past Year
  • Issues: 0
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  • HenrikBengtsson (57)
  • hannanw (2)
  • arostamianfar (1)
  • lima1 (1)
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  • ramaniak (1)
  • gaiusjaugustus (1)
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  • lima1 (1)
  • gara-z (1)
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bug (21) enhancement (18) help wanted (15) wontfix (4) question (3) CRAN Policy (3)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 911 last-month
  • Total docker downloads: 14,442
  • Total dependent packages: 4
  • Total dependent repositories: 11
  • Total versions: 35
  • Total maintainers: 1
cran.r-project.org: PSCBS

Analysis of Parent-Specific DNA Copy Numbers

  • Versions: 35
  • Dependent Packages: 4
  • Dependent Repositories: 11
  • Downloads: 911 Last month
  • Docker Downloads: 14,442
Rankings
Dependent repos count: 8.7%
Dependent packages count: 9.3%
Forks count: 12.2%
Average: 14.1%
Docker downloads count: 15.9%
Downloads: 19.1%
Stargazers count: 19.3%
Maintainers (1)
henrikb@braju.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • DNAcopy >= 1.42.0 imports
  • R.cache >= 0.15.0 imports
  • R.methodsS3 >= 1.8.1 imports
  • R.oo >= 1.24.0 imports
  • R.utils >= 2.11.0 imports
  • aroma.light >= 2.4.0 imports
  • future >= 1.22.1 imports
  • grDevices * imports
  • graphics * imports
  • listenv >= 0.8.0 imports
  • matrixStats >= 0.61.0 imports
  • parallel * imports
  • stats * imports
  • utils * imports
  • Hmisc * suggests
  • R.devices >= 2.17.0 suggests
  • R.rsp >= 0.44.0 suggests
  • ggplot2 >= 3.2.1 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
.github/workflows/covr.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite