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Question about --nbr_fracs #64
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Hi there,
Thanks for trying conga! This is a really interesting question. I can see that using larger neighbor-fractions for building the neighbor lists might lead to more significant P values in some cases, but I wonder whether one might lose some "specificity" and see more generic assocations, like the tendency for CD4+ (or CD8+) TCRs to be more similar to one another, or for memory TCRs to share sequence features, versus TCR/GEX associations in smaller groups of cells. I don't think there's any correct answer. Note that the default suggestion is to combine both 0.01 and 0.1 neighbor fractions.
Take care,
Phil
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Subject: [phbradley/conga] Question about --nbr_fracs (Issue #64)
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Hi everyone,
A wonderful package to link scRNA and scTCR!!
Recently I test the run_conga.py script and found that CoNGA scores in TCR2D was easily influenced by argument 'nbr_fracs'. When I use the default option (0.01)(above), it seems that less association between gex and tcr. If I set to 0.5 (below), obvious association was present. And you emphasized the smalllish nbr_fracs in your script. So is there any suggestions in selecting the suitable value for nbr_fracs?
by the way, is the "length" in TCR.csv necessary for analyses? I have a TCR.csv file without "length" (It is not standard output from 10x). I want to include this file in CoNGA input.
Looking forward to your reply. Thanks!
[merge_graph_vs_graph_logos]<https://urldefense.com/v3/__https://user-images.githubusercontent.com/40140273/270259679-4c3e684b-ea14-440d-9274-4307125c77c2.png__;!!GuAItXPztq0!mbI3vzLg3tBe4orrTMtgNPBrKUQB4xYO1jsODHYzd4ZQQrGXYSVorzxSiVkeLyPXoQKfQ1zi-eDxyPka_1AJ4tPW$>
[test1_graph_vs_graph_logos]<https://urldefense.com/v3/__https://user-images.githubusercontent.com/40140273/270259693-21355921-55ba-4e1e-9530-d2f7cf2f99f0.png__;!!GuAItXPztq0!mbI3vzLg3tBe4orrTMtgNPBrKUQB4xYO1jsODHYzd4ZQQrGXYSVorzxSiVkeLyPXoQKfQ1zi-eDxyPka_2tf-tfa$>
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Thanks for your sugguestions! Thanks again for your reply |
Re: 1485 vs 1500, it probably depends on your dataset, and there may not be much difference. Generally speaking, cells with the same clonotype do tend to have similar GEX profiles, which supports conga's reduction to clonotypes. But in a dynamic setting there can be substantial heterogeneity. Regarding the logos, the genes themselves are probably getting written out somewhere to a TSV file. But the TCR logos also don't look good, so it might be worth fixing that and then seeing if the DEGs are more interpretable. I think the problem is with the conversion from SVG to PNG. If you attach the log file, maybe we could figure out which tool is being used and swap it out for something that performs better on your system. I find Inkscape to be the most reliable across linux and mac. |
An excellent suggestion!! |
Hi everyone,
A wonderful package to link scRNA and scTCR!!
Recently I test the run_conga.py script and found that CoNGA scores in TCR2D was easily influenced by argument 'nbr_fracs'. When I use the default option (0.01)(above), it seems that less association between gex and tcr. If I set to 0.5 (below), obvious association was present. And you emphasized the smalllish nbr_fracs in your script. So is there any suggestions in selecting the suitable value for nbr_fracs?
by the way, is the "length" in TCR.csv necessary for analyses? I have a TCR.csv file without "length" (It is not standard output from 10x). I want to include this file in CoNGA input.
Looking forward to your reply. Thanks!
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