CNV calling, copy number calling, using ONLY Log2R values (with segmentation
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7 days ago
jcn • 0

Hello all,

I have two data files with the following columns: File 1, CGH_Probe_Table: Probe Name, Chromosome, Start, Stop, Feature Number, Log Ratio. File 2, SNP_Probe_Table: SNP ID, Probe Name, Chromosome, SNP Position, Feature number, Genotype.

My ultimate goal is to call copy numbers using this data, as well as do some grouping/segmenting of genic regions to find copy number change boundaries.. I am fairly new to this, so I would appreciate any help on how to calculate b-allele frequency (if possible, I don't think I have enough info in my files to do this), calling copy numbers based on logR2 while also segmenting areas of like copy numbers. Thanks!

log2R copy calling segmentation number cnv • 109 views
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R package Dnacopy and its CBS algorithm can solve it

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