TY - JOUR
T1 - SNPchip
T2 - R classes and methods for SNP array data
AU - Scharpf, Robert B.
AU - Ting, Jason C.
AU - Pevsner, Jonathan
AU - Ruczinski, Ingo
N1 - Funding Information:
Institute of Environmental Health Sciences (P. I. Thomas Louis) and grant DMS034211 from the National Science Foundation (P. I. Giovanni Parmigiani). J.P. was supported by NIH grants R01 HD046598 and MRDDRC HD24061. I.R. was supported by NIH grant CA074841.
PY - 2007/3
Y1 - 2007/3
N2 - Summary: High-density single nucleotide polymorphism microarrays (SNP chips) provide information on a subject's genome, such as copy number and genotype (heterozygosity/homozygosity) at a SNP. While fluorescence in situ hybridization and karyotyping reveal many abnormalities, SNP chips provide a higher resolution map of the human genome that can be used to detect, e.g., aneuploidies, microdeletions, microduplications and loss of heterozygosity (LOH). As a variety of diseases are linked to such chromosomal abnormalities, SNP chips promise new insights for these diseases by aiding in the discovery of such regions, and may suggest targets for intervention. The R package SNPchip contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.
AB - Summary: High-density single nucleotide polymorphism microarrays (SNP chips) provide information on a subject's genome, such as copy number and genotype (heterozygosity/homozygosity) at a SNP. While fluorescence in situ hybridization and karyotyping reveal many abnormalities, SNP chips provide a higher resolution map of the human genome that can be used to detect, e.g., aneuploidies, microdeletions, microduplications and loss of heterozygosity (LOH). As a variety of diseases are linked to such chromosomal abnormalities, SNP chips promise new insights for these diseases by aiding in the discovery of such regions, and may suggest targets for intervention. The R package SNPchip contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.
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U2 - 10.1093/bioinformatics/btl638
DO - 10.1093/bioinformatics/btl638
M3 - Article
C2 - 17204461
AN - SCOPUS:34047098908
SN - 1367-4803
VL - 23
SP - 627
EP - 628
JO - Bioinformatics
JF - Bioinformatics
IS - 5
ER -