Rseg-an R package to optimize segmentation of SNP array data

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Rseg-an R package to optimize segmentation of SNP array data. / Lamy, Philippe; Wiuf, Carsten; Ørntoft, Torben F.; Andersen, Claus L.

In: Bioinformatics, Vol. 27, No. 3, btq668, 01.02.2011, p. 419-420.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Lamy, P, Wiuf, C, Ørntoft, TF & Andersen, CL 2011, 'Rseg-an R package to optimize segmentation of SNP array data', Bioinformatics, vol. 27, no. 3, btq668, pp. 419-420. https://doi.org/10.1093/bioinformatics/btq668

APA

Lamy, P., Wiuf, C., Ørntoft, T. F., & Andersen, C. L. (2011). Rseg-an R package to optimize segmentation of SNP array data. Bioinformatics, 27(3), 419-420. [btq668]. https://doi.org/10.1093/bioinformatics/btq668

Vancouver

Lamy P, Wiuf C, Ørntoft TF, Andersen CL. Rseg-an R package to optimize segmentation of SNP array data. Bioinformatics. 2011 Feb 1;27(3):419-420. btq668. https://doi.org/10.1093/bioinformatics/btq668

Author

Lamy, Philippe ; Wiuf, Carsten ; Ørntoft, Torben F. ; Andersen, Claus L. / Rseg-an R package to optimize segmentation of SNP array data. In: Bioinformatics. 2011 ; Vol. 27, No. 3. pp. 419-420.

Bibtex

@article{45a872e001fe4f8cb58b8e3f5e5b8133,
title = "Rseg-an R package to optimize segmentation of SNP array data",
abstract = "Summary: The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples. Results: We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts.",
author = "Philippe Lamy and Carsten Wiuf and {\O}rntoft, {Torben F.} and Andersen, {Claus L.}",
year = "2011",
month = feb,
day = "1",
doi = "10.1093/bioinformatics/btq668",
language = "English",
volume = "27",
pages = "419--420",
journal = "Bioinformatics (Online)",
issn = "1367-4811",
publisher = "Oxford University Press",
number = "3",

}

RIS

TY - JOUR

T1 - Rseg-an R package to optimize segmentation of SNP array data

AU - Lamy, Philippe

AU - Wiuf, Carsten

AU - Ørntoft, Torben F.

AU - Andersen, Claus L.

PY - 2011/2/1

Y1 - 2011/2/1

N2 - Summary: The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples. Results: We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts.

AB - Summary: The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples. Results: We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts.

UR - http://www.scopus.com/inward/record.url?scp=79551598515&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btq668

DO - 10.1093/bioinformatics/btq668

M3 - Journal article

C2 - 21134892

AN - SCOPUS:79551598515

VL - 27

SP - 419

EP - 420

JO - Bioinformatics (Online)

JF - Bioinformatics (Online)

SN - 1367-4811

IS - 3

M1 - btq668

ER -

ID: 203899400