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Using the R Package crlmm for Genotyping and Copy Number Estimation


Scharpf, RB; Irizarry, RA; Ritchie, ME; Carvalho, B; Ruczinski, I
2011-04-01
JOURNAL OF STATISTICAL SOFTWARE
Journal Article
40
12
1-32
Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workfow for the estimation of allele-specific copy number and integration of the marker-level estimates with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R
JOURNAL STATISTICAL SOFTWARE
ARRAY CGH DATA; CIRCULAR BINARY SEGMENTATION; HIDDEN MARKOV-MODELS; SNP ARRAYS; GENOME; ALGORITHM; NORMALIZATION; EXPLORATION; SOFTWARE; IMPACT
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Creation Date 2011-04-01 12:00:00