Enrichment Overview
Last updated: 2024-01-23
Checks: 7 0
Knit directory: dgrp-starve/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | dd3c95c | nklimko | 2024-01-23 | wflow_publish(“analysis/enrich.Rmd”) |
Dive back in:
We left off looking to modify the selection cutoff for top terms. While various ideas were floated(standard devs, percentiles, flat cutoff), there was not a consistently most useful method for looking at both male and female data. As such, I opted to run a series of flat cutoffs(100, 50, 25) for both complete methods per sex.
I first looked at the top terms ordered to look for patterns in the data. While I’m unsure of the significance, the clustering of correlations for top terms shares a shape within sexes across methods. Notably, female data had a sharper increase(negative slope) for top results
load('snake/data/go/50_tables/enrichment.Rdata')
topGrid <- function(data, sex, psize, custom.title, custom.Xlab, custom.Ylab){
plothole <- ggplot(data, aes(x=index, y=cor, label=term))+
geom_point(color=viridis(1, begin=0.5), size=psize)+
theme_minimal() +
labs(x=custom.Xlab, y=custom.Ylab, tag=sex, title=custom.title) +
theme(text=element_text(size=10), plot.tag = element_text(size=15))
return(plothole)
}
gg[[1]] <- topGrid(blupF, 'F', 1, 'Top Female Results: TBLUP', 'Rank', 'Correlation')
gg[[2]] <- topGrid(blupM, 'M', 1, 'Top Male Results: TBLUP', 'Rank', 'Correlation')
gg[[3]] <- topGrid(bayesF, 'F', 1, 'Top Female Results: BayesC', 'Rank', 'Correlation')
gg[[4]] <- topGrid(bayesM, 'M', 1, 'Top Male Results: BayesC', 'Rank', 'Correlation')
plot_grid(gg[[1]], gg[[2]], gg[[3]], gg[[4]], ncol=2)
After this, I found the correlation between the two methods to see how similar generated results are.
Female Overall
Female Top 200
Male Overall
Male Top 100
Moving past this, I wanted to assess the effect of term count on enrichment
load("snake/data/go/50_tables/enrich/kables.Rdata")
kable(bayesF_Kable, caption="Female BayesC", "simple")| Flybase Gene | Count | Gene | Flybase Gene | Count | Gene | Flybase Gene | Count | Gene |
|---|---|---|---|---|---|---|---|---|
| FBgn0262738 | 15 | norpA | FBgn0025595 | 9 | AkhR | FBgn0025595 | 8 | AkhR |
| FBgn0003731 | 13 | Egfr | FBgn0003731 | 9 | Egfr | FBgn0000575 | 6 | emc |
| FBgn0004635 | 13 | rho | FBgn0003205 | 9 | Ras85D | FBgn0004552 | 4 | Akh |
| FBgn0003205 | 10 | Ras85D | FBgn0004635 | 9 | rho | FBgn0283499 | 4 | InR |
| FBgn0025595 | 9 | AkhR | FBgn0000575 | 7 | emc | FBgn0000490 | 4 | dpp |
| FBgn0003310 | 8 | NULL | FBgn0262738 | 7 | norpA | FBgn0010303 | 3 | hep |
| FBgn0000575 | 7 | emc | FBgn0004552 | 5 | Akh | FBgn0015279 | 3 | Pi3K92E |
| FBgn0015795 | 7 | Rab7 | FBgn0015279 | 5 | Pi3K92E | FBgn0033799 | 3 | GLaz |
| FBgn0283499 | 6 | InR | FBgn0283499 | 5 | InR | FBgn0036449 | 3 | bmm |
| FBgn0039114 | 6 | Lsd-1 | FBgn0003310 | 5 | NULL | FBgn0003731 | 3 | Egfr |
| FBgn0004552 | 5 | Akh | FBgn0035586 | 4 | CG10671 | FBgn0003205 | 3 | Ras85D |
| FBgn0015279 | 5 | Pi3K92E | FBgn0026252 | 4 | msk | FBgn0003463 | 3 | sog |
| FBgn0035586 | 5 | CG10671 | FBgn0000490 | 4 | dpp | FBgn0003719 | 3 | tld |
| FBgn0003463 | 5 | sog | FBgn0261648 | 4 | salm | FBgn0262738 | 3 | norpA |
| FBgn0003719 | 5 | tld | FBgn0010303 | 3 | hep | NA | NA | NA |
| FBgn0036545 | 5 | GXIVsPLA2 | FBgn0036046 | 3 | Ilp2 | NA | NA | NA |
| FBgn0039655 | 5 | CG14507 | FBgn0024248 | 3 | chico | NA | NA | NA |
| FBgn0003118 | 5 | pnt | FBgn0033799 | 3 | GLaz | NA | NA | NA |
| FBgn0005672 | 5 | spi | FBgn0036449 | 3 | bmm | NA | NA | NA |
| FBgn0036046 | 4 | Ilp2 | FBgn0036260 | 3 | Rh7 | NA | NA | NA |
| FBgn0003651 | 4 | svp | FBgn0003463 | 3 | sog | NA | NA | NA |
| FBgn0010379 | 4 | Akt1 | FBgn0003719 | 3 | tld | NA | NA | NA |
| FBgn0024248 | 4 | chico | FBgn0003984 | 3 | vn | NA | NA | NA |
| FBgn0036449 | 4 | bmm | FBgn0038197 | 3 | foxo | NA | NA | NA |
| FBgn0026252 | 4 | msk | FBgn0039114 | 3 | Lsd-1 | NA | NA | NA |
| FBgn0036260 | 4 | Rh7 | FBgn0003218 | 3 | rdgB | NA | NA | NA |
| FBgn0000490 | 4 | dpp | FBgn0026207 | 3 | mbo | NA | NA | NA |
| FBgn0003984 | 4 | vn | FBgn0027537 | 3 | Nup93-1 | NA | NA | NA |
| FBgn0261648 | 4 | salm | FBgn0031078 | 3 | Nup205 | NA | NA | NA |
| FBgn0029720 | 4 | CG3009 | FBgn0033737 | 3 | Nup54 | NA | NA | NA |
| FBgn0030013 | 4 | GIIIspla2 | FBgn0033766 | 3 | CG8771 | NA | NA | NA |
| FBgn0033170 | 4 | sPLA2 | FBgn0038274 | 3 | Nup93-2 | NA | NA | NA |
| FBgn0050503 | 4 | CG30503 | FBgn0061200 | 3 | Nup153 | NA | NA | NA |
| FBgn0250862 | 4 | CG42237 | FBgn0003256 | 3 | rl | NA | NA | NA |
| FBgn0003218 | 4 | rdgB | FBgn0034140 | 3 | Lst | NA | NA | NA |
| FBgn0030608 | 4 | Lsd-2 | FBgn0015795 | 3 | Rab7 | NA | NA | NA |
| FBgn0035206 | 4 | CG9186 | FBgn0002940 | 3 | ninaE | NA | NA | NA |
| FBgn0040336 | 4 | Seipin | FBgn0003295 | 3 | ru | NA | NA | NA |
| FBgn0026207 | 4 | mbo | NA | NA | NA | NA | NA | NA |
| FBgn0004435 | 4 | Galphaq | NA | NA | NA | NA | NA | NA |
| FBgn0000257 | 4 | car | NA | NA | NA | NA | NA | NA |
| FBgn0000482 | 4 | dor | NA | NA | NA | NA | NA | NA |
| FBgn0003256 | 4 | rl | NA | NA | NA | NA | NA | NA |
| FBgn0035871 | 4 | BI-1 | NA | NA | NA | NA | NA | NA |
| FBgn0052350 | 4 | Vps11 | NA | NA | NA | NA | NA | NA |
| FBgn0285911 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0015754 | 4 | Lis-1 | NA | NA | NA | NA | NA | NA |
| FBgn0004647 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0002940 | 4 | ninaE | NA | NA | NA | NA | NA | NA |
| FBgn0003295 | 4 | ru | NA | NA | NA | NA | NA | NA |
| FBgn0020386 | 4 | Pdk1 | NA | NA | NA | NA | NA | NA |
| FBgn0262451 | 4 | ban | NA | NA | NA | NA | NA | NA |
| FBgn0004784 | 4 | inaC | NA | NA | NA | NA | NA | NA |
| FBgn0003169 | 3 | put | NA | NA | NA | NA | NA | NA |
| FBgn0010303 | 3 | hep | NA | NA | NA | NA | NA | NA |
| FBgn0028717 | 3 | Lnk | NA | NA | NA | NA | NA | NA |
| FBgn0010051 | 3 | Itp-r83A | NA | NA | NA | NA | NA | NA |
| FBgn0030607 | 3 | dob | NA | NA | NA | NA | NA | NA |
| FBgn0033226 | 3 | CG1882 | NA | NA | NA | NA | NA | NA |
| FBgn0033799 | 3 | GLaz | NA | NA | NA | NA | NA | NA |
| FBgn0262103 | 3 | Sik3 | NA | NA | NA | NA | NA | NA |
| FBgn0002576 | 3 | lz | NA | NA | NA | NA | NA | NA |
| FBgn0004885 | 3 | tok | NA | NA | NA | NA | NA | NA |
| FBgn0050418 | 3 | nord | NA | NA | NA | NA | NA | NA |
| FBgn0039152 | 3 | Root | NA | NA | NA | NA | NA | NA |
| FBgn0038197 | 3 | foxo | NA | NA | NA | NA | NA | NA |
| FBgn0028741 | 3 | fab1 | NA | NA | NA | NA | NA | NA |
| FBgn0029870 | 3 | Marf | NA | NA | NA | NA | NA | NA |
| FBgn0052703 | 3 | Erk7 | NA | NA | NA | NA | NA | NA |
| FBgn0027537 | 3 | Nup93-1 | NA | NA | NA | NA | NA | NA |
| FBgn0031078 | 3 | Nup205 | NA | NA | NA | NA | NA | NA |
| FBgn0033737 | 3 | Nup54 | NA | NA | NA | NA | NA | NA |
| FBgn0033766 | 3 | CG8771 | NA | NA | NA | NA | NA | NA |
| FBgn0038274 | 3 | Nup93-2 | NA | NA | NA | NA | NA | NA |
| FBgn0061200 | 3 | Nup153 | NA | NA | NA | NA | NA | NA |
| FBgn0261549 | 3 | rdgA | NA | NA | NA | NA | NA | NA |
| FBgn0002566 | 3 | lt | NA | NA | NA | NA | NA | NA |
| FBgn0034140 | 3 | Lst | NA | NA | NA | NA | NA | NA |
| FBgn0038659 | 3 | EndoA | NA | NA | NA | NA | NA | NA |
| FBgn0086676 | 3 | spin | NA | NA | NA | NA | NA | NA |
| FBgn0015721 | 3 | ktub | NA | NA | NA | NA | NA | NA |
| FBgn0086687 | 3 | Desat1 | NA | NA | NA | NA | NA | NA |
| FBgn0014010 | 3 | Rab5 | NA | NA | NA | NA | NA | NA |
| FBgn0025680 | 3 | cry | NA | NA | NA | NA | NA | NA |
| FBgn0038167 | 3 | Lkb1 | NA | NA | NA | NA | NA | NA |
| FBgn0004611 | 3 | Plc21C | NA | NA | NA | NA | NA | NA |
| FBgn0001263 | 3 | inaD | NA | NA | NA | NA | NA | NA |
| FBgn0052699 | 3 | LPCAT | NA | NA | NA | NA | NA | NA |
| FBgn0265048 | 3 | cv-d | NA | NA | NA | NA | NA | NA |
kable(bayesF_Kable, caption="Male BayesC", "simple")| Flybase Gene | Count | Gene | Flybase Gene | Count | Gene | Flybase Gene | Count | Gene |
|---|---|---|---|---|---|---|---|---|
| FBgn0262738 | 15 | norpA | FBgn0025595 | 9 | AkhR | FBgn0025595 | 8 | AkhR |
| FBgn0003731 | 13 | Egfr | FBgn0003731 | 9 | Egfr | FBgn0000575 | 6 | emc |
| FBgn0004635 | 13 | rho | FBgn0003205 | 9 | Ras85D | FBgn0004552 | 4 | Akh |
| FBgn0003205 | 10 | Ras85D | FBgn0004635 | 9 | rho | FBgn0283499 | 4 | InR |
| FBgn0025595 | 9 | AkhR | FBgn0000575 | 7 | emc | FBgn0000490 | 4 | dpp |
| FBgn0003310 | 8 | NULL | FBgn0262738 | 7 | norpA | FBgn0010303 | 3 | hep |
| FBgn0000575 | 7 | emc | FBgn0004552 | 5 | Akh | FBgn0015279 | 3 | Pi3K92E |
| FBgn0015795 | 7 | Rab7 | FBgn0015279 | 5 | Pi3K92E | FBgn0033799 | 3 | GLaz |
| FBgn0283499 | 6 | InR | FBgn0283499 | 5 | InR | FBgn0036449 | 3 | bmm |
| FBgn0039114 | 6 | Lsd-1 | FBgn0003310 | 5 | NULL | FBgn0003731 | 3 | Egfr |
| FBgn0004552 | 5 | Akh | FBgn0035586 | 4 | CG10671 | FBgn0003205 | 3 | Ras85D |
| FBgn0015279 | 5 | Pi3K92E | FBgn0026252 | 4 | msk | FBgn0003463 | 3 | sog |
| FBgn0035586 | 5 | CG10671 | FBgn0000490 | 4 | dpp | FBgn0003719 | 3 | tld |
| FBgn0003463 | 5 | sog | FBgn0261648 | 4 | salm | FBgn0262738 | 3 | norpA |
| FBgn0003719 | 5 | tld | FBgn0010303 | 3 | hep | NA | NA | NA |
| FBgn0036545 | 5 | GXIVsPLA2 | FBgn0036046 | 3 | Ilp2 | NA | NA | NA |
| FBgn0039655 | 5 | CG14507 | FBgn0024248 | 3 | chico | NA | NA | NA |
| FBgn0003118 | 5 | pnt | FBgn0033799 | 3 | GLaz | NA | NA | NA |
| FBgn0005672 | 5 | spi | FBgn0036449 | 3 | bmm | NA | NA | NA |
| FBgn0036046 | 4 | Ilp2 | FBgn0036260 | 3 | Rh7 | NA | NA | NA |
| FBgn0003651 | 4 | svp | FBgn0003463 | 3 | sog | NA | NA | NA |
| FBgn0010379 | 4 | Akt1 | FBgn0003719 | 3 | tld | NA | NA | NA |
| FBgn0024248 | 4 | chico | FBgn0003984 | 3 | vn | NA | NA | NA |
| FBgn0036449 | 4 | bmm | FBgn0038197 | 3 | foxo | NA | NA | NA |
| FBgn0026252 | 4 | msk | FBgn0039114 | 3 | Lsd-1 | NA | NA | NA |
| FBgn0036260 | 4 | Rh7 | FBgn0003218 | 3 | rdgB | NA | NA | NA |
| FBgn0000490 | 4 | dpp | FBgn0026207 | 3 | mbo | NA | NA | NA |
| FBgn0003984 | 4 | vn | FBgn0027537 | 3 | Nup93-1 | NA | NA | NA |
| FBgn0261648 | 4 | salm | FBgn0031078 | 3 | Nup205 | NA | NA | NA |
| FBgn0029720 | 4 | CG3009 | FBgn0033737 | 3 | Nup54 | NA | NA | NA |
| FBgn0030013 | 4 | GIIIspla2 | FBgn0033766 | 3 | CG8771 | NA | NA | NA |
| FBgn0033170 | 4 | sPLA2 | FBgn0038274 | 3 | Nup93-2 | NA | NA | NA |
| FBgn0050503 | 4 | CG30503 | FBgn0061200 | 3 | Nup153 | NA | NA | NA |
| FBgn0250862 | 4 | CG42237 | FBgn0003256 | 3 | rl | NA | NA | NA |
| FBgn0003218 | 4 | rdgB | FBgn0034140 | 3 | Lst | NA | NA | NA |
| FBgn0030608 | 4 | Lsd-2 | FBgn0015795 | 3 | Rab7 | NA | NA | NA |
| FBgn0035206 | 4 | CG9186 | FBgn0002940 | 3 | ninaE | NA | NA | NA |
| FBgn0040336 | 4 | Seipin | FBgn0003295 | 3 | ru | NA | NA | NA |
| FBgn0026207 | 4 | mbo | NA | NA | NA | NA | NA | NA |
| FBgn0004435 | 4 | Galphaq | NA | NA | NA | NA | NA | NA |
| FBgn0000257 | 4 | car | NA | NA | NA | NA | NA | NA |
| FBgn0000482 | 4 | dor | NA | NA | NA | NA | NA | NA |
| FBgn0003256 | 4 | rl | NA | NA | NA | NA | NA | NA |
| FBgn0035871 | 4 | BI-1 | NA | NA | NA | NA | NA | NA |
| FBgn0052350 | 4 | Vps11 | NA | NA | NA | NA | NA | NA |
| FBgn0285911 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0015754 | 4 | Lis-1 | NA | NA | NA | NA | NA | NA |
| FBgn0004647 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0002940 | 4 | ninaE | NA | NA | NA | NA | NA | NA |
| FBgn0003295 | 4 | ru | NA | NA | NA | NA | NA | NA |
| FBgn0020386 | 4 | Pdk1 | NA | NA | NA | NA | NA | NA |
| FBgn0262451 | 4 | ban | NA | NA | NA | NA | NA | NA |
| FBgn0004784 | 4 | inaC | NA | NA | NA | NA | NA | NA |
| FBgn0003169 | 3 | put | NA | NA | NA | NA | NA | NA |
| FBgn0010303 | 3 | hep | NA | NA | NA | NA | NA | NA |
| FBgn0028717 | 3 | Lnk | NA | NA | NA | NA | NA | NA |
| FBgn0010051 | 3 | Itp-r83A | NA | NA | NA | NA | NA | NA |
| FBgn0030607 | 3 | dob | NA | NA | NA | NA | NA | NA |
| FBgn0033226 | 3 | CG1882 | NA | NA | NA | NA | NA | NA |
| FBgn0033799 | 3 | GLaz | NA | NA | NA | NA | NA | NA |
| FBgn0262103 | 3 | Sik3 | NA | NA | NA | NA | NA | NA |
| FBgn0002576 | 3 | lz | NA | NA | NA | NA | NA | NA |
| FBgn0004885 | 3 | tok | NA | NA | NA | NA | NA | NA |
| FBgn0050418 | 3 | nord | NA | NA | NA | NA | NA | NA |
| FBgn0039152 | 3 | Root | NA | NA | NA | NA | NA | NA |
| FBgn0038197 | 3 | foxo | NA | NA | NA | NA | NA | NA |
| FBgn0028741 | 3 | fab1 | NA | NA | NA | NA | NA | NA |
| FBgn0029870 | 3 | Marf | NA | NA | NA | NA | NA | NA |
| FBgn0052703 | 3 | Erk7 | NA | NA | NA | NA | NA | NA |
| FBgn0027537 | 3 | Nup93-1 | NA | NA | NA | NA | NA | NA |
| FBgn0031078 | 3 | Nup205 | NA | NA | NA | NA | NA | NA |
| FBgn0033737 | 3 | Nup54 | NA | NA | NA | NA | NA | NA |
| FBgn0033766 | 3 | CG8771 | NA | NA | NA | NA | NA | NA |
| FBgn0038274 | 3 | Nup93-2 | NA | NA | NA | NA | NA | NA |
| FBgn0061200 | 3 | Nup153 | NA | NA | NA | NA | NA | NA |
| FBgn0261549 | 3 | rdgA | NA | NA | NA | NA | NA | NA |
| FBgn0002566 | 3 | lt | NA | NA | NA | NA | NA | NA |
| FBgn0034140 | 3 | Lst | NA | NA | NA | NA | NA | NA |
| FBgn0038659 | 3 | EndoA | NA | NA | NA | NA | NA | NA |
| FBgn0086676 | 3 | spin | NA | NA | NA | NA | NA | NA |
| FBgn0015721 | 3 | ktub | NA | NA | NA | NA | NA | NA |
| FBgn0086687 | 3 | Desat1 | NA | NA | NA | NA | NA | NA |
| FBgn0014010 | 3 | Rab5 | NA | NA | NA | NA | NA | NA |
| FBgn0025680 | 3 | cry | NA | NA | NA | NA | NA | NA |
| FBgn0038167 | 3 | Lkb1 | NA | NA | NA | NA | NA | NA |
| FBgn0004611 | 3 | Plc21C | NA | NA | NA | NA | NA | NA |
| FBgn0001263 | 3 | inaD | NA | NA | NA | NA | NA | NA |
| FBgn0052699 | 3 | LPCAT | NA | NA | NA | NA | NA | NA |
| FBgn0265048 | 3 | cv-d | NA | NA | NA | NA | NA | NA |
kable(bayesF_Kable, caption="Female TBLUP", "simple")| Flybase Gene | Count | Gene | Flybase Gene | Count | Gene | Flybase Gene | Count | Gene |
|---|---|---|---|---|---|---|---|---|
| FBgn0262738 | 15 | norpA | FBgn0025595 | 9 | AkhR | FBgn0025595 | 8 | AkhR |
| FBgn0003731 | 13 | Egfr | FBgn0003731 | 9 | Egfr | FBgn0000575 | 6 | emc |
| FBgn0004635 | 13 | rho | FBgn0003205 | 9 | Ras85D | FBgn0004552 | 4 | Akh |
| FBgn0003205 | 10 | Ras85D | FBgn0004635 | 9 | rho | FBgn0283499 | 4 | InR |
| FBgn0025595 | 9 | AkhR | FBgn0000575 | 7 | emc | FBgn0000490 | 4 | dpp |
| FBgn0003310 | 8 | NULL | FBgn0262738 | 7 | norpA | FBgn0010303 | 3 | hep |
| FBgn0000575 | 7 | emc | FBgn0004552 | 5 | Akh | FBgn0015279 | 3 | Pi3K92E |
| FBgn0015795 | 7 | Rab7 | FBgn0015279 | 5 | Pi3K92E | FBgn0033799 | 3 | GLaz |
| FBgn0283499 | 6 | InR | FBgn0283499 | 5 | InR | FBgn0036449 | 3 | bmm |
| FBgn0039114 | 6 | Lsd-1 | FBgn0003310 | 5 | NULL | FBgn0003731 | 3 | Egfr |
| FBgn0004552 | 5 | Akh | FBgn0035586 | 4 | CG10671 | FBgn0003205 | 3 | Ras85D |
| FBgn0015279 | 5 | Pi3K92E | FBgn0026252 | 4 | msk | FBgn0003463 | 3 | sog |
| FBgn0035586 | 5 | CG10671 | FBgn0000490 | 4 | dpp | FBgn0003719 | 3 | tld |
| FBgn0003463 | 5 | sog | FBgn0261648 | 4 | salm | FBgn0262738 | 3 | norpA |
| FBgn0003719 | 5 | tld | FBgn0010303 | 3 | hep | NA | NA | NA |
| FBgn0036545 | 5 | GXIVsPLA2 | FBgn0036046 | 3 | Ilp2 | NA | NA | NA |
| FBgn0039655 | 5 | CG14507 | FBgn0024248 | 3 | chico | NA | NA | NA |
| FBgn0003118 | 5 | pnt | FBgn0033799 | 3 | GLaz | NA | NA | NA |
| FBgn0005672 | 5 | spi | FBgn0036449 | 3 | bmm | NA | NA | NA |
| FBgn0036046 | 4 | Ilp2 | FBgn0036260 | 3 | Rh7 | NA | NA | NA |
| FBgn0003651 | 4 | svp | FBgn0003463 | 3 | sog | NA | NA | NA |
| FBgn0010379 | 4 | Akt1 | FBgn0003719 | 3 | tld | NA | NA | NA |
| FBgn0024248 | 4 | chico | FBgn0003984 | 3 | vn | NA | NA | NA |
| FBgn0036449 | 4 | bmm | FBgn0038197 | 3 | foxo | NA | NA | NA |
| FBgn0026252 | 4 | msk | FBgn0039114 | 3 | Lsd-1 | NA | NA | NA |
| FBgn0036260 | 4 | Rh7 | FBgn0003218 | 3 | rdgB | NA | NA | NA |
| FBgn0000490 | 4 | dpp | FBgn0026207 | 3 | mbo | NA | NA | NA |
| FBgn0003984 | 4 | vn | FBgn0027537 | 3 | Nup93-1 | NA | NA | NA |
| FBgn0261648 | 4 | salm | FBgn0031078 | 3 | Nup205 | NA | NA | NA |
| FBgn0029720 | 4 | CG3009 | FBgn0033737 | 3 | Nup54 | NA | NA | NA |
| FBgn0030013 | 4 | GIIIspla2 | FBgn0033766 | 3 | CG8771 | NA | NA | NA |
| FBgn0033170 | 4 | sPLA2 | FBgn0038274 | 3 | Nup93-2 | NA | NA | NA |
| FBgn0050503 | 4 | CG30503 | FBgn0061200 | 3 | Nup153 | NA | NA | NA |
| FBgn0250862 | 4 | CG42237 | FBgn0003256 | 3 | rl | NA | NA | NA |
| FBgn0003218 | 4 | rdgB | FBgn0034140 | 3 | Lst | NA | NA | NA |
| FBgn0030608 | 4 | Lsd-2 | FBgn0015795 | 3 | Rab7 | NA | NA | NA |
| FBgn0035206 | 4 | CG9186 | FBgn0002940 | 3 | ninaE | NA | NA | NA |
| FBgn0040336 | 4 | Seipin | FBgn0003295 | 3 | ru | NA | NA | NA |
| FBgn0026207 | 4 | mbo | NA | NA | NA | NA | NA | NA |
| FBgn0004435 | 4 | Galphaq | NA | NA | NA | NA | NA | NA |
| FBgn0000257 | 4 | car | NA | NA | NA | NA | NA | NA |
| FBgn0000482 | 4 | dor | NA | NA | NA | NA | NA | NA |
| FBgn0003256 | 4 | rl | NA | NA | NA | NA | NA | NA |
| FBgn0035871 | 4 | BI-1 | NA | NA | NA | NA | NA | NA |
| FBgn0052350 | 4 | Vps11 | NA | NA | NA | NA | NA | NA |
| FBgn0285911 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0015754 | 4 | Lis-1 | NA | NA | NA | NA | NA | NA |
| FBgn0004647 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0002940 | 4 | ninaE | NA | NA | NA | NA | NA | NA |
| FBgn0003295 | 4 | ru | NA | NA | NA | NA | NA | NA |
| FBgn0020386 | 4 | Pdk1 | NA | NA | NA | NA | NA | NA |
| FBgn0262451 | 4 | ban | NA | NA | NA | NA | NA | NA |
| FBgn0004784 | 4 | inaC | NA | NA | NA | NA | NA | NA |
| FBgn0003169 | 3 | put | NA | NA | NA | NA | NA | NA |
| FBgn0010303 | 3 | hep | NA | NA | NA | NA | NA | NA |
| FBgn0028717 | 3 | Lnk | NA | NA | NA | NA | NA | NA |
| FBgn0010051 | 3 | Itp-r83A | NA | NA | NA | NA | NA | NA |
| FBgn0030607 | 3 | dob | NA | NA | NA | NA | NA | NA |
| FBgn0033226 | 3 | CG1882 | NA | NA | NA | NA | NA | NA |
| FBgn0033799 | 3 | GLaz | NA | NA | NA | NA | NA | NA |
| FBgn0262103 | 3 | Sik3 | NA | NA | NA | NA | NA | NA |
| FBgn0002576 | 3 | lz | NA | NA | NA | NA | NA | NA |
| FBgn0004885 | 3 | tok | NA | NA | NA | NA | NA | NA |
| FBgn0050418 | 3 | nord | NA | NA | NA | NA | NA | NA |
| FBgn0039152 | 3 | Root | NA | NA | NA | NA | NA | NA |
| FBgn0038197 | 3 | foxo | NA | NA | NA | NA | NA | NA |
| FBgn0028741 | 3 | fab1 | NA | NA | NA | NA | NA | NA |
| FBgn0029870 | 3 | Marf | NA | NA | NA | NA | NA | NA |
| FBgn0052703 | 3 | Erk7 | NA | NA | NA | NA | NA | NA |
| FBgn0027537 | 3 | Nup93-1 | NA | NA | NA | NA | NA | NA |
| FBgn0031078 | 3 | Nup205 | NA | NA | NA | NA | NA | NA |
| FBgn0033737 | 3 | Nup54 | NA | NA | NA | NA | NA | NA |
| FBgn0033766 | 3 | CG8771 | NA | NA | NA | NA | NA | NA |
| FBgn0038274 | 3 | Nup93-2 | NA | NA | NA | NA | NA | NA |
| FBgn0061200 | 3 | Nup153 | NA | NA | NA | NA | NA | NA |
| FBgn0261549 | 3 | rdgA | NA | NA | NA | NA | NA | NA |
| FBgn0002566 | 3 | lt | NA | NA | NA | NA | NA | NA |
| FBgn0034140 | 3 | Lst | NA | NA | NA | NA | NA | NA |
| FBgn0038659 | 3 | EndoA | NA | NA | NA | NA | NA | NA |
| FBgn0086676 | 3 | spin | NA | NA | NA | NA | NA | NA |
| FBgn0015721 | 3 | ktub | NA | NA | NA | NA | NA | NA |
| FBgn0086687 | 3 | Desat1 | NA | NA | NA | NA | NA | NA |
| FBgn0014010 | 3 | Rab5 | NA | NA | NA | NA | NA | NA |
| FBgn0025680 | 3 | cry | NA | NA | NA | NA | NA | NA |
| FBgn0038167 | 3 | Lkb1 | NA | NA | NA | NA | NA | NA |
| FBgn0004611 | 3 | Plc21C | NA | NA | NA | NA | NA | NA |
| FBgn0001263 | 3 | inaD | NA | NA | NA | NA | NA | NA |
| FBgn0052699 | 3 | LPCAT | NA | NA | NA | NA | NA | NA |
| FBgn0265048 | 3 | cv-d | NA | NA | NA | NA | NA | NA |
kable(bayesF_Kable, caption="Male TBLUP", "simple")| Flybase Gene | Count | Gene | Flybase Gene | Count | Gene | Flybase Gene | Count | Gene |
|---|---|---|---|---|---|---|---|---|
| FBgn0262738 | 15 | norpA | FBgn0025595 | 9 | AkhR | FBgn0025595 | 8 | AkhR |
| FBgn0003731 | 13 | Egfr | FBgn0003731 | 9 | Egfr | FBgn0000575 | 6 | emc |
| FBgn0004635 | 13 | rho | FBgn0003205 | 9 | Ras85D | FBgn0004552 | 4 | Akh |
| FBgn0003205 | 10 | Ras85D | FBgn0004635 | 9 | rho | FBgn0283499 | 4 | InR |
| FBgn0025595 | 9 | AkhR | FBgn0000575 | 7 | emc | FBgn0000490 | 4 | dpp |
| FBgn0003310 | 8 | NULL | FBgn0262738 | 7 | norpA | FBgn0010303 | 3 | hep |
| FBgn0000575 | 7 | emc | FBgn0004552 | 5 | Akh | FBgn0015279 | 3 | Pi3K92E |
| FBgn0015795 | 7 | Rab7 | FBgn0015279 | 5 | Pi3K92E | FBgn0033799 | 3 | GLaz |
| FBgn0283499 | 6 | InR | FBgn0283499 | 5 | InR | FBgn0036449 | 3 | bmm |
| FBgn0039114 | 6 | Lsd-1 | FBgn0003310 | 5 | NULL | FBgn0003731 | 3 | Egfr |
| FBgn0004552 | 5 | Akh | FBgn0035586 | 4 | CG10671 | FBgn0003205 | 3 | Ras85D |
| FBgn0015279 | 5 | Pi3K92E | FBgn0026252 | 4 | msk | FBgn0003463 | 3 | sog |
| FBgn0035586 | 5 | CG10671 | FBgn0000490 | 4 | dpp | FBgn0003719 | 3 | tld |
| FBgn0003463 | 5 | sog | FBgn0261648 | 4 | salm | FBgn0262738 | 3 | norpA |
| FBgn0003719 | 5 | tld | FBgn0010303 | 3 | hep | NA | NA | NA |
| FBgn0036545 | 5 | GXIVsPLA2 | FBgn0036046 | 3 | Ilp2 | NA | NA | NA |
| FBgn0039655 | 5 | CG14507 | FBgn0024248 | 3 | chico | NA | NA | NA |
| FBgn0003118 | 5 | pnt | FBgn0033799 | 3 | GLaz | NA | NA | NA |
| FBgn0005672 | 5 | spi | FBgn0036449 | 3 | bmm | NA | NA | NA |
| FBgn0036046 | 4 | Ilp2 | FBgn0036260 | 3 | Rh7 | NA | NA | NA |
| FBgn0003651 | 4 | svp | FBgn0003463 | 3 | sog | NA | NA | NA |
| FBgn0010379 | 4 | Akt1 | FBgn0003719 | 3 | tld | NA | NA | NA |
| FBgn0024248 | 4 | chico | FBgn0003984 | 3 | vn | NA | NA | NA |
| FBgn0036449 | 4 | bmm | FBgn0038197 | 3 | foxo | NA | NA | NA |
| FBgn0026252 | 4 | msk | FBgn0039114 | 3 | Lsd-1 | NA | NA | NA |
| FBgn0036260 | 4 | Rh7 | FBgn0003218 | 3 | rdgB | NA | NA | NA |
| FBgn0000490 | 4 | dpp | FBgn0026207 | 3 | mbo | NA | NA | NA |
| FBgn0003984 | 4 | vn | FBgn0027537 | 3 | Nup93-1 | NA | NA | NA |
| FBgn0261648 | 4 | salm | FBgn0031078 | 3 | Nup205 | NA | NA | NA |
| FBgn0029720 | 4 | CG3009 | FBgn0033737 | 3 | Nup54 | NA | NA | NA |
| FBgn0030013 | 4 | GIIIspla2 | FBgn0033766 | 3 | CG8771 | NA | NA | NA |
| FBgn0033170 | 4 | sPLA2 | FBgn0038274 | 3 | Nup93-2 | NA | NA | NA |
| FBgn0050503 | 4 | CG30503 | FBgn0061200 | 3 | Nup153 | NA | NA | NA |
| FBgn0250862 | 4 | CG42237 | FBgn0003256 | 3 | rl | NA | NA | NA |
| FBgn0003218 | 4 | rdgB | FBgn0034140 | 3 | Lst | NA | NA | NA |
| FBgn0030608 | 4 | Lsd-2 | FBgn0015795 | 3 | Rab7 | NA | NA | NA |
| FBgn0035206 | 4 | CG9186 | FBgn0002940 | 3 | ninaE | NA | NA | NA |
| FBgn0040336 | 4 | Seipin | FBgn0003295 | 3 | ru | NA | NA | NA |
| FBgn0026207 | 4 | mbo | NA | NA | NA | NA | NA | NA |
| FBgn0004435 | 4 | Galphaq | NA | NA | NA | NA | NA | NA |
| FBgn0000257 | 4 | car | NA | NA | NA | NA | NA | NA |
| FBgn0000482 | 4 | dor | NA | NA | NA | NA | NA | NA |
| FBgn0003256 | 4 | rl | NA | NA | NA | NA | NA | NA |
| FBgn0035871 | 4 | BI-1 | NA | NA | NA | NA | NA | NA |
| FBgn0052350 | 4 | Vps11 | NA | NA | NA | NA | NA | NA |
| FBgn0285911 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0015754 | 4 | Lis-1 | NA | NA | NA | NA | NA | NA |
| FBgn0004647 | 4 | NULL | NA | NA | NA | NA | NA | NA |
| FBgn0002940 | 4 | ninaE | NA | NA | NA | NA | NA | NA |
| FBgn0003295 | 4 | ru | NA | NA | NA | NA | NA | NA |
| FBgn0020386 | 4 | Pdk1 | NA | NA | NA | NA | NA | NA |
| FBgn0262451 | 4 | ban | NA | NA | NA | NA | NA | NA |
| FBgn0004784 | 4 | inaC | NA | NA | NA | NA | NA | NA |
| FBgn0003169 | 3 | put | NA | NA | NA | NA | NA | NA |
| FBgn0010303 | 3 | hep | NA | NA | NA | NA | NA | NA |
| FBgn0028717 | 3 | Lnk | NA | NA | NA | NA | NA | NA |
| FBgn0010051 | 3 | Itp-r83A | NA | NA | NA | NA | NA | NA |
| FBgn0030607 | 3 | dob | NA | NA | NA | NA | NA | NA |
| FBgn0033226 | 3 | CG1882 | NA | NA | NA | NA | NA | NA |
| FBgn0033799 | 3 | GLaz | NA | NA | NA | NA | NA | NA |
| FBgn0262103 | 3 | Sik3 | NA | NA | NA | NA | NA | NA |
| FBgn0002576 | 3 | lz | NA | NA | NA | NA | NA | NA |
| FBgn0004885 | 3 | tok | NA | NA | NA | NA | NA | NA |
| FBgn0050418 | 3 | nord | NA | NA | NA | NA | NA | NA |
| FBgn0039152 | 3 | Root | NA | NA | NA | NA | NA | NA |
| FBgn0038197 | 3 | foxo | NA | NA | NA | NA | NA | NA |
| FBgn0028741 | 3 | fab1 | NA | NA | NA | NA | NA | NA |
| FBgn0029870 | 3 | Marf | NA | NA | NA | NA | NA | NA |
| FBgn0052703 | 3 | Erk7 | NA | NA | NA | NA | NA | NA |
| FBgn0027537 | 3 | Nup93-1 | NA | NA | NA | NA | NA | NA |
| FBgn0031078 | 3 | Nup205 | NA | NA | NA | NA | NA | NA |
| FBgn0033737 | 3 | Nup54 | NA | NA | NA | NA | NA | NA |
| FBgn0033766 | 3 | CG8771 | NA | NA | NA | NA | NA | NA |
| FBgn0038274 | 3 | Nup93-2 | NA | NA | NA | NA | NA | NA |
| FBgn0061200 | 3 | Nup153 | NA | NA | NA | NA | NA | NA |
| FBgn0261549 | 3 | rdgA | NA | NA | NA | NA | NA | NA |
| FBgn0002566 | 3 | lt | NA | NA | NA | NA | NA | NA |
| FBgn0034140 | 3 | Lst | NA | NA | NA | NA | NA | NA |
| FBgn0038659 | 3 | EndoA | NA | NA | NA | NA | NA | NA |
| FBgn0086676 | 3 | spin | NA | NA | NA | NA | NA | NA |
| FBgn0015721 | 3 | ktub | NA | NA | NA | NA | NA | NA |
| FBgn0086687 | 3 | Desat1 | NA | NA | NA | NA | NA | NA |
| FBgn0014010 | 3 | Rab5 | NA | NA | NA | NA | NA | NA |
| FBgn0025680 | 3 | cry | NA | NA | NA | NA | NA | NA |
| FBgn0038167 | 3 | Lkb1 | NA | NA | NA | NA | NA | NA |
| FBgn0004611 | 3 | Plc21C | NA | NA | NA | NA | NA | NA |
| FBgn0001263 | 3 | inaD | NA | NA | NA | NA | NA | NA |
| FBgn0052699 | 3 | LPCAT | NA | NA | NA | NA | NA | NA |
| FBgn0265048 | 3 | cv-d | NA | NA | NA | NA | NA | NA |
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.5 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /opt/ohpc/pub/libs/gnu9/openblas/0.3.7/lib/libopenblasp-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.31 kableExtra_1.3.4 knitr_1.43 reshape2_1.4.4
[5] melt_1.10.0 ggcorrplot_0.1.4.1 lubridate_1.9.3 forcats_1.0.0
[9] stringr_1.5.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[13] tibble_3.2.1 tidyverse_2.0.0 scales_1.2.1 viridis_0.6.4
[17] viridisLite_0.4.2 qqman_0.1.9 cowplot_1.1.1 ggplot2_3.4.4
[21] data.table_1.14.8 dplyr_1.1.3 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] httr_1.4.7 sass_0.4.7 jsonlite_1.8.7 bslib_0.5.0
[5] getPass_0.2-2 highr_0.10 yaml_2.3.7 pillar_1.9.0
[9] glue_1.6.2 digest_0.6.33 promises_1.2.0.1 rvest_1.0.3
[13] colorspace_2.1-0 htmltools_0.5.5 httpuv_1.6.12 plyr_1.8.9
[17] pkgconfig_2.0.3 calibrate_1.7.7 webshot_0.5.5 processx_3.8.2
[21] svglite_2.1.2 whisker_0.4.1 later_1.3.1 tzdb_0.4.0
[25] timechange_0.2.0 git2r_0.32.0 generics_0.1.3 farver_2.1.1
[29] cachem_1.0.8 withr_2.5.0 cli_3.6.1 magrittr_2.0.3
[33] evaluate_0.21 ps_1.7.5 fs_1.6.3 fansi_1.0.4
[37] MASS_7.3-60 xml2_1.3.3 tools_4.1.2 hms_1.1.3
[41] lifecycle_1.0.3 munsell_0.5.0 callr_3.7.3 compiler_4.1.2
[45] jquerylib_0.1.4 systemfonts_1.0.5 rlang_1.1.1 grid_4.1.2
[49] rstudioapi_0.15.0 htmlwidgets_1.6.2 labeling_0.4.3 rmarkdown_2.23
[53] gtable_0.3.4 R6_2.5.1 gridExtra_2.3 fastmap_1.1.1
[57] utf8_1.2.3 rprojroot_2.0.3 stringi_1.7.12 Rcpp_1.0.11
[61] vctrs_0.6.4 tidyselect_1.2.0 xfun_0.39