UpSetR wrapper for sigora results
sigora_upsetR(sigora_res, GPStable, ...)
Arguments
| sigora_res |
Object returned by the sigoraWrappR function |
| GPStable |
Object returned by makeGPS_wrappR function, setting dev=TRUE |
| ... |
other parameters to upset |
Examples
sigora_res <- prora::sigora_example
GPStable <- prora::GPStab
sigora_upsetR(sigora_res, GPStable)
#> Joining, by = "pathwayId"
#> Joining, by = "gene"
df <- get_UniprotID_from_fasta_header(prora::exampleContrastData)
myGPSrepo <- makeGPS_wrappR(ids = df$UniprotID)
#> 'select()' returned 1:many mapping between keys and columns
#> Joining, by = "pathwayID"
#> Time difference of 0.674825 secs
#> Time difference of 1.163109 secs
names(myGPSrepo)
#> [1] "gps" "gpsTable"
res <- sigoraWrappR(df,score_col = "estimate", GPSrepos = myGPSrepo$gps,
threshold = 0.5)
#> pathwy.id description pvalues Bonferroni
#> 1 03010 Ribosome 1.143e-221 1.532e-219
#> 2 03060 Protein export 1.008e-15 1.351e-13
#> 3 04141 Protein processing in endoplasmic reticulum 4.155e-10 5.568e-08
#> 4 05160 Hepatitis C 2.422e-08 3.245e-06
#> 5 04144 Endocytosis 2.813e-07 3.769e-05
#> 6 04530 Tight junction 2.479e-06 3.322e-04
#> 7 04510 Focal adhesion 3.521e-06 4.718e-04
#> 8 04114 Oocyte meiosis 3.458e-05 4.634e-03
#> 9 04360 Axon guidance 3.606e-05 4.832e-03
#> successes PathwaySize N sample.size
#> 1 654.12 1577.52 27971.51 3192.29
#> 2 39.27 83.71 27971.51 3192.29
#> 3 340.68 2176.34 27971.51 3192.29
#> 4 36.99 119.34 27971.51 3192.29
#> 5 343.99 2334.53 27971.51 3192.29
#> 6 82.61 432.19 27971.51 3192.29
#> 7 37.00 149.14 27971.51 3192.29
#> 8 30.88 122.42 27971.51 3192.29
#> 9 27.62 104.61 27971.51 3192.29
sigora_upsetR(res, myGPSrepo$gpsTable)
#> Joining, by = "pathwayId"
#> Joining, by = "gene"
