Closed RuimeiL closed 9 months ago
@RuimeiL Hi, thanks for your questions. Could you put more details?
for example cn <- read_copynumber(segTabs_own, seg_cols = c("chromosome", "start", "end", "segVal"), genome_build = "hg38", complement = FALSE, verbose = TRUE)
cn_tally_W <- sig_tally(cn, method = "W") sig_w <- sig_extract(cn_tally_W$nmf_matrix, n_sig = ?)
n_sig = ?, I can set any number here. n_sig =1,2,3,4,5......
How are the confidence scores of these signatures ranked? how many signatures are recommended for selection? Thank you for your time.
Hi @RuimeiL , please roughly read the documentation https://shixiangwang.github.io/sigminer-book/index.html (PART 1 and 2 specifically) and https://cran.r-project.org/web/packages/sigminer/vignettes/cnsignature.html
If you don't have the concept of extracting signatures (signature types and basic operations, difference between signature extraction and fitting) and setting the parameters, you cannot do the correct analysis.
For your specific questions, you can find the answer at https://shixiangwang.github.io/sigminer-book/basic-workflow.html#de-novo-signature-discovery
Thank you so much!
Hello, when using Sigminer for CNV (Copy Number Variation) and SV (Structural Variation) signature analysis, the selection allows me to choose n signatures. How are the confidence scores of these signatures ranked? Is there a scoring system? Typically, how many signatures are recommended for selection?