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 1.2.4

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crlmm-package Genotype Calling via CRLMM Algorithm
calls Accessors for Calls and Confidences on a SnpSet object
calls,SnpSet-method Accessors for Calls and Confidences on a SnpSet object
celDates Extract dates from the cel file header
cnrma Quantile normalizes the intensities for the nonpolymorphic probe to a HapMap reference distribution.
computeCopynumber Computes copy number
confs Accessors for Calls and Confidences on a SnpSet object
confs,SnpSet-method Accessors for Calls and Confidences on a SnpSet object
crlmm Genotype oligonucleotide arrays with CRLMM
crlmmIllumina Genotype Illumina Infinium II BeadChip data with CRLMM
list.celfiles List CEL files.
readIdatFiles Reads Idat Files from Infinium II Illumina BeadChips
snprma Preprocessing tool for SNP arrays.