Entering edit mode
18 months ago
melissachua90
▴
60
I ran the GrnBoost2 algorithm on my bulk transcriptomics data and now want to predict regulon using cisTarget. My code raised "could not convert string to float: " error.
ADJACENCIES_FNAME:
| TF | Target | Importance | |
|---|---|---|---|
| 0 | ZFY | DDX3Y | 271.644764 |
| 1 | ZFY | EIF1AY | 249.632524 |
| 2 | ZFY | CYorf15A | 249.479488 |
| 3 | ZFY | USP9Y | 242.145026 |
| 4 | ZFY | KDM5D | 215.670768 |
Run pySCENIC:
!pyscenic ctx {ADJACENCIES_FNAME} {DBS_PARAM} \
--annotations_fname {MOTIF_ANNOTATIONS_FNAME} \
--expression_mtx_fname {EXP_MTX_QC_FNAME} \
--output {MOTIFS_FNAME} \
--num_workers 26
Traceback:
2022-10-04 13:49:42,020 - pyscenic.cli.pyscenic - INFO - Creating modules.
2022-10-04 13:49:47,486 - pyscenic.cli.pyscenic - ERROR - could not convert string to float:
