Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

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Documentation for package ‘crlmm’ version 1.8.11

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crlmm-package Genotype Calling via CRLMM Algorithm
CA Accessors for allele-specific or total copy number
CA-method crlmm methods for class "CNSet"
CB Accessors for allele-specific or total copy number
CB-method crlmm methods for class "CNSet"
celDates Extract dates from the cel file header
constructIlluminaCNSet Construct an instance of CNSetLM after preprocessing Illumina files
corr Accessors for batch-specific summary statistics.
corr-method Methods for class "AssayData" in crlmm
corr-method crlmm methods for class "CNSet"
crlmm Genotype oligonucleotide arrays with CRLMM
crlmm2 Genotype oligonucleotide arrays with CRLMM
crlmmCopynumber Locus- and allele-specific estimation of copy number
crlmmCopynumber2 Locus- and allele-specific estimation of copy number
crlmmCopynumberLD Locus- and allele-specific estimation of copy number
crlmmIllumina Genotype Illumina Infinium II BeadChip data with CRLMM
crlmmIlluminaV2 Read and Genotype Illumina Infinium II BeadChip data with CRLMM
genotype Preprocessing and genotyping of Affymetrix arrays.
genotype2 Preprocessing and genotyping of Affymetrix arrays.
genotypeLD Preprocessing and genotyping of Affymetrix arrays.
lines-method crlmm methods for class "CNSet"
mads Accessors for batch-specific summary statistics.
mads-method Methods for class "AssayData" in crlmm
mads-method crlmm methods for class "CNSet"
medians Accessors for batch-specific summary statistics.
medians-method Methods for class "AssayData" in crlmm
medians-method crlmm methods for class "CNSet"
Ns Accessors for batch-specific summary statistics.
Ns-method Methods for class "AssayData" in crlmm
Ns-method crlmm methods for class "CNSet"
nuA Accessors for allele-specific or total copy number
nuA-method crlmm methods for class "CNSet"
nuB Accessors for allele-specific or total copy number
nuB-method crlmm methods for class "CNSet"
phiA Accessors for allele-specific or total copy number
phiA-method crlmm methods for class "CNSet"
phiB Accessors for allele-specific or total copy number
phiB-method crlmm methods for class "CNSet"
readIdatFiles Reads Idat Files from Infinium II Illumina BeadChips
readIdatFiles2 Reads Idat Files from Infinium II Illumina BeadChips
sample.CNSetLM Dataset of class 'CNSetLM'
snprma Preprocessing tool for SNP arrays.
snprma2 Preprocessing tool for SNP arrays.
tau2 Accessors for batch-specific summary statistics.
tau2-method Methods for class "AssayData" in crlmm
tau2-method crlmm methods for class "CNSet"
totalCopynumber Accessors for allele-specific or total copy number
totalCopynumber-method crlmm methods for class "CNSet"