File Format Conversion (GO::TermFinder to wide format)
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4.5 years ago
Yean ▴ 140

Hi all,

I Just did GO Enrichment using GO::TermFinder via API (I need to perform via API due to reproducible code) and the report is something like

The following gene(s) will be considered:

YDL235C YPD1
YDL224C WHI4
YDL225W SHS1
YDL226C GCS1
YDL227C HO
YDL228C YDL228C
YDL229W SSB1
YDL230W PTP1
YDL231C BRE4
YDL232W OST4
YDL233W YDL233W
YDL234C GYP7

Finding terms for P


Finding terms for C


Finding terms for F

-- 1 of 15--
GOID    GO:0005096
TERM    GTPase activator activity
CORRECTED P-VALUE       0.0113038452336839
UNCORRECTED P-VALUE     0.00113038452336839
NUM_ANNOTATIONS 2 of 12 in the list, vs 31 of 7272 in the genome
The genes annotated to this node are:
YDL234C, YDL226C
-- 2 of 15--
GOID    GO:0008047
TERM    enzyme activator activity
CORRECTED P-VALUE       0.0316194107645226
UNCORRECTED P-VALUE     0.00316194107645226
NUM_ANNOTATIONS 2 of 12 in the list, vs 52 of 7272 in the genome
The genes annotated to this node are:
YDL234C, YDL226C

I am struggling to convert such format to wide format

GOID TERM CORRECTED P-VALUE UNCORRECTED P-VALUE The genes annotated to this node are:
GO:0005096 GTPase activator activity  0.0113 0.0011 YDL234C,YDL226C
GO:0008047 enzyme activator activity   0.031 0.0031  YDL234C,YDL226C

Any suggestion ? (bash and R are preferable)

Many Thanks for Help :)

GO::TermFinder • 543 views
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