Closed smdn-tt closed 1 year ago
Hi @smdn-tt, Thank you for your appreciation.
I am in need of the consensus plots which look like typical ascat/battenberg CN profiles, but this file does not seem to have been created.
Can you help me understand which type of plot you are referring to, with an example figure? I will be happy to help you generate it.
A second question- the output file CNAmtx.Rdata does not have any rownames, how do I determine which chromosome location the scores represent for each cell? I am seeking to identify cells based on specific CN changes that I know are present from my WGS.
You can find the row annotations in the SAMPLE_NAME_count_mtx_annot.RData file.
Thank you for your speedy reply! The consensus figure is this one from the first tutorial. I am not certain if i need to include an additional option in my command?
And thank you for pointing to the row annotations.
Solange
Thank you for your speedy reply! The consensus figure is this one from the first tutorial. I am not certain if i need to include an additional option in my command?
And thank you for pointing to the row annotations.
Solange
I corrected it in the last commit 802f8c1, now if you reinstall SCEVAN and re-run pipelineCNA you can get the consensus plot.
Let me know if everything is OK now. Regards.
Works perfectly now, thank you!
Greetings and thank you for this amazing package which has sped up my analyses significantly. I have run SCEVAN on a human tumour single nuclear dataset (10x), and the results are comparable with the WGS findings. However, I am in need of the consensus plots which look like typical ascat/battenberg CN profiles, but this file does not seem to have been created.
My code was as follows:
results <- SCEVAN::pipelineCNA(count_mtx = rawcts, norm_cell = normcells, sample = "OS10", par_cores = 6, SUBCLONES = TRUE)
My output folder contains the following:
list.files("./output/")
[1] " OS10 vega_output" " OS10_SubcloneDiffAnalysis.RData" " OS10onlytumor vega_output"[4] "OS10_Clonal_CN.seg" "OS10_CNAmtx.RData" "OS10_CNAmtxSubclones.RData"
[7] "OS10_count_mtx_annot.RData" "OS10_subclone1_CN.seg" "OS10_subclone2_CN.seg"
[10] "OS10_subclone3_CN.seg" "OS10-DEchr1-182393-6520061_subclones.png" "OS10CloneTree.png"
[13] "OS10heatmap_subclones.png" "OS10heatmap.png" "OS10OncoHeat.png"
[16] "OS10OncoHeat2.png" "OS10onlytumorheatmap.png" "OS10pathwayAnalysis_subclones1.png"
[19] "OS10pathwayAnalysis_subclones2.png" "OS10pathwayAnalysis_subclones3.png" "OS10tsne_CNA.png"
[22] "OS10tsne_scRNA.png"
I have SCEVAN 1.0.1 installed (running on R4.1.2)
A second question- the output file CNAmtx.Rdata does not have any rownames, how do I determine which chromosome location the scores represent for each cell? I am seeking to identify cells based on specific CN changes that I know are present from my WGS.
Your assistance is much appreciated!
Solange