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martinjzhang / scDRS

Single-cell disease relevance score (scDRS)
https://martinjzhang.github.io/scDRS/
MIT License
98 stars 11 forks source link

munge-gs input format #61

Closed DonaldSandoz2000 closed 1 year ago

DonaldSandoz2000 commented 1 year ago

--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.

Hi, when I'm using munge-gs to process a gene set csv file for a trait, it only reads all the rows, but it doesn't seem to be able to distinguish the two columns well, is there a mistake in the formatting of my csv file somewhere?

martinjzhang commented 1 year ago

Hi @DonaldSandoz2000 ,

scDRS uses .tsv files instead of .csv files https://martinjzhang.github.io/scDRS/file_format.html

Martin

DonaldSandoz2000 commented 1 year ago

Oh, I made a stupid mistake. My previous tsv export in R didn't have tabs to separate the two columns. Now I've corrected it and I've got the result I wanted! Thank you so much for your answer.