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
APA
Vancouver
Author
Bibtex
}
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