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ccagc / QDNAseq

QDNAseq package for Bioconductor
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mutiple ref while using "compareToReference" #63

Open jiading opened 5 years ago

jiading commented 5 years ago

Hi,

I would like to use QDNAseq with Reference samples. I read in 1 tumor, and 10 normal samples in bam files.

Shall I use command like: tumorVsNormal <- compareToReference(copyNumbersSmooth, 10)

Thanks, Jia

JocelynSP commented 4 years ago

Hi Jia,

I see this question is from 8 months ago, so I guess you worked it out! I think you need to make 10 versions of 'tumorVsNormal'. If the tumor sample is the first sample in copyNumbersSmooth: tumorVsNormal1 <- compareToReference( copyNumbersSmooth, c( 2, NA, rep( FALSE, 9 ) ) ) ( divide sample 1 (tumor) by sample 2 (1st normal), keep sample 2 unchanged, discard the rest) tumorVsNormal2 <- compareToReference( copyNumbersSmooth, c( 3, F, NA, rep( FALSE, 8 ) ) ) ( divide sample 1 by sample 3, keep sample 3 unchanged, discard the rest) etc.

Regards, Jocelyn