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tiroshlab / 3ca

Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
MIT License
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How to prepare the Genes_nmf_w_basis_example.RDS for generating MPs? #4

Open Lualululu opened 1 year ago

Lualululu commented 1 year ago

Input:

Genes_nmf_w_basis is a list in which each entry contains NMF gene-scores of a single sample. In our study we ran NMF using ranks 4-9 on the top 7000 genes in each sample. Hence each entry in Genes_nmf_w_basis is a matrix with 7000 rows (genes) X 39 columns (NMF programs)

Generate_Meta_Programs.R generates MPs from NMFs programs that were calculated for each sample using different ranks. The NMF programs were calculated per sample using the ‘NMF’ R package: NMFs_per_sample = nmf(x = Expression_matrix, rank = 4:9, method="snmf/r", nrun = 10) NMF programs are listed in Genes_nmf_w_basis, where each entry contains NMF gene-scores of a single sample.

  1. "Using ranks 4-9 on the top 7000 genes in each sample" How to choose the top 7000 genes? Does this mean that the top 7000 for each rank are the same?

  2. “NMF gene-scores” How to calculate the NMF gene-scores?

3.How to correlate cells with their corresponding MP? Do different MP correspond to different cell subtypes?

alievakrash commented 3 months ago

Hi, I am also trying to link the NMFs to the MPs, I go the Table 2 from the paper, but is there any additional data to check which of the Robust NMFs were assigned to which MP? Thanks!

lisch7 commented 5 days ago

Hi, Do you know the reasoning behind generating 39 programs for each tumor? What is the rationale behind the number 39? Thanks!

Phoenix12580 commented 3 days ago

Hi, 嗨， Do you know the reasoning behind generating 39 programs for each tumor? What is the rationale behind the number 39?您知道为什么为每个肿瘤生成 39 个程序背后的原因吗？39 这个数字的依据是什么？ Thanks! 谢谢！

rank = 4:9 4+6+7+8+9就是39了