Camoco
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Published
20 hours ago •
LinkageIO
LinkageIO
Gene name hyphens get filtered out when using cob.from_table()
If I have a data matrix that looks like this to serve as input into COB.from_table.
| R1M-C2 | R2M-C2 | R3M-C2 | R1T-C2 |
|---|---|---|---|
| BDIBD21-3.1G0000700 | 0.440474 | 0.255481 | 0.312441 |
| BDIBD21-3.1G0000800 | 1.41546 | 2.19172 | 2.00877 |
| BDIBD21-3.1G0000900 | 0.0210054 | 0 | 0.0714931 |
| BDIBD21-3.1G0001000 | 0 | 0 | 0 |
That command converts the gene names to something like BDIBD213.1G000290 before testing membership where the hyphen gets removed. This change ends up filtering out all of the genes since they don't match the RefGen gene names that include the hyphen.
