Problem with munging

[HJ234]

Hi, Thank you for the great program. I'm trying to run scDRS on one trait, but I seem to get no gene sets after munging with scdrs munge-gs

Call: scdrs munge-gs \
--zscore-file SLE.genes.out.zstat.tsv \
--weight zscore \
--n-min 10 \
--n-max 1000 \
--out-file munge_top1000Z.gs

--zscore-file loaded: n_gene=19025, n_trait=1 (sys_time=0.0s)
Print info for the first 3 traits and first 10 genes
Traits               ['SLE']
SAMD11               [1.037]
NOC2L                [1.1508]
KLHL17               [1.5457]
PLEKHN1              [2.8403]
PERM1                [3.0402]
HES4                 [2.3732]
ISG15                [2.2022]
AGRN                 [2.7473]
RNF223               [2.6844]
C1orf159             [3.9652]
--zscore-file have values above 1 or below 0. Seems fine.

Finish munging 1 gene sets (sys_time=0.0s)

The resulting file looks like the following

Would you know what the problem is? Thanks

[martinjzhang]

Hi,

Thank you for reporting this issue. I couldn't identify the cause based on just the .log file. Could you send us a minimal reproducible example (e.g., your zscore file) and also let us know which version of scDRS you are using?

[HJ234]

Hi, thanks for the quick reply. I've sent the zstat file I've been using to "jinyezhang@hsph.harvard.edu" and I'm using scDRS 1.0.2.

[martinjzhang]

Hi @HJ234

Thank you for sharing the .zscore file. I ran scdrs munge-gs on your .zscore file but couldn't reproduce the issue. I sent you the code and the generated .gs file via email.

This suggests that your zscore file is fine. But I am afraid I still couldn't identify the cause of the issue. Are you using Linux? Could you try to reinstall scDRS using virtualenv (e.g., https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1588662166 for a tutorial)? If the issue persists, I can push a version of scDRS with more diagnostic information and ask you to run the new version on your data to hopefully identify the issue.

[HJ234]

Hi Martin,

Thank you for sending me over the .gs file. I've fixed the issue now, but still don't know what the problem was. I haven't changed anything since last time but it seems to work now. Sorry I can't provide you with analytics and suggest any causes at the moment. I'm getting really interesting results from the down stream analysis though, so thank you very much for developing the program and I hope there's more features to come.

[martinjzhang]

Thank you @HJ234 and good to hear that you are getting interesting results. We are actively developing the packages. I hope we can release some cool features real soon!

[DonaldSandoz2000]

Hi, Thank you for the great program. I'm trying to run scDRS on one trait, but I seem to get no gene sets after munging with scdrs munge-gs

Call: scdrs munge-gs \
--zscore-file SLE.genes.out.zstat.tsv \
--weight zscore \
--n-min 10 \
--n-max 1000 \
--out-file munge_top1000Z.gs

--zscore-file loaded: n_gene=19025, n_trait=1 (sys_time=0.0s)
Print info for the first 3 traits and first 10 genes
Traits               ['SLE']
SAMD11               [1.037]
NOC2L                [1.1508]
KLHL17               [1.5457]
PLEKHN1              [2.8403]
PERM1                [3.0402]
HES4                 [2.3732]
ISG15                [2.2022]
AGRN                 [2.7473]
RNF223               [2.6844]
C1orf159             [3.9652]
--zscore-file have values above 1 or below 0. Seems fine.

Finish munging 1 gene sets (sys_time=0.0s)

The resulting file looks like the following

Would you know what the problem is? Thanks

--zscore-file loaded: n_gene=62787, n_trait=0 (sys_time=0.0s) Print info for the first 3 traits and first 10 genes Traits [] PSRC1,-9.289225811 [] AL592148.3,-7.992844093 [] MIA3,-7.120338886 [] TCF21,-6.520148163 [] SLC22A1,-6.220870419 [] NOS3,-6.197266755 [] NBEAL1,-6.112940111 [] ICA1L,6.017449523 [] LIPA,5.811769649 [] AL359922.2,5.799499614 [] Warning: zscore-file values are all between 0 and 1. Do you know what causes this?