Re: Codex2 query: norm_index

[Jiang, Yuchao]

Hi,

Yes it’s not unexpected that you would also get CNVs from the normal samples. These are presumably the germline CNVs. If you want to focus on the CNVs in the control samples, just focus on sample 5.

Yuchao

On Mar 21, 2020, at 7:49 AM, vineeta singh <vineetas...@gmail.com> wrote:

Dear Doctor, 

Am using Codex2 for the CNV analysis but on giving normal index its doesn't seems to be working. I have 5 samples named as sample_1, sample_2, sample_3, sample_4, sample_5. Among these 5 samples sample_1, sample_2, sample_3, samle_4 are as Normal controls and sample_5 as Test samples. 

In below function I have specified normal index as given below but in final CNV list am getting CNV from sample_2, sample_3 and sample_5. Instead I want CNVs from sample_5 only. 

bamFile <- list.files(pattern = '*.bam$')
bamdir <- file.path(bamFile)
sampname <- substr(bamFile,1,8)
sampname
bedFile <- file.path("TSOne Expanded_BED_v2.bed")
bambedObj <- getbambed(bamdir = bamdir, bedFile = bedFile,
                       sampname = sampname, projectname = "CODEX2_demo")
######################################################

norm_index_demo <- c(1,2,3,4)
normObj <- normalize_codex2_ns(Y_qc = Y_qc[chr.index,],
                               gc_qc = gc_qc[chr.index],
                               K = 1:2, norm_index = norm_index_demo ,
                               N = N)

Kindly help in this regards. 

Thanks & Regards,

Vineeta Singh

[vineeta singh]

Thanks for the response. 

If this is normal then I guess will consider only CNV from sample 5. I have tried giving 2 normal samples then it giving CNV from sample_5 only. This pattern I tried with Codex library. With Codex2 yet to be tried.

Thanks

Vineeta Singh