DeepSEA (estimated separately)
A data.frame: 19 × 4
| logRR | lower_bound | upper_bound | annota |
|---|
| <dbl> | <dbl> | <dbl> | <chr> |
|---|
| 1 | 0.152345316 | 0.034860271 | 0.2698304 | ago_adult_brain.BA4.hg19_uniform_prior |
|---|
| 6 | 0.141263118 | -0.004271118 | 0.2867974 | ago_adult_brain.Cingulate.gyrus.hg19_uniform_prior |
|---|
| 7 | 0.143252450 | -0.024612957 | 0.3111179 | elavl_Adult_brain.all_human_samples.hg19_uniform_prior |
|---|
| 8 | 0.124226054 | -0.058436047 | 0.3068882 | elavl_Adult_brain.BA9_Alzheimer.hg19_uniform_prior |
|---|
| 12 | 0.187983653 | -0.061409708 | 0.4373770 | alt3.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 22 | 0.231823744 | 0.060244700 | 0.4034028 | alt3.spliced.exon.5SS.hg19_uniform_prior |
|---|
| 32 | 0.007018262 | -0.603579614 | 0.6176161 | alt5.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 42 | 0.103746287 | -0.320931834 | 0.5284244 | alt5.spliced.exon.5SS.hg19_uniform_prior |
|---|
| 52 | 0.184812435 | -0.068472935 | 0.4380978 | branchpoint_cell.line_HeLa.K562.hg19_uniform_prior |
|---|
| 62 | 0.141202727 | -0.197226998 | 0.4796325 | cass.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 13 | 0.172829456 | -0.082525545 | 0.4281845 | cass.spliced.exon.5SS.hg19_uniform_prior |
|---|
| 23 | 0.270818616 | 0.137095265 | 0.4045420 | iret.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 33 | 0.252194150 | 0.088490341 | 0.4158980 | iret.spliced.exon.5SS.hg19_uniform_prior |
|---|
| 43 | 0.223077987 | 0.023244392 | 0.4229116 | mutx.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 53 | 0.177127582 | -0.066693191 | 0.4209484 | mutx.spliced.exon.5SS.hg19_uniform_prior |
|---|
| 63 | 0.120831357 | -0.306291219 | 0.5479539 | SS3.constitutive_genome_ensembl.with.CLIP.genes.hg19_uniform_prior |
|---|
| 71 | 0.229779223 | 0.038195358 | 0.4213631 | SS5.constitutive_genome_ensembl.with.CLIP.genes.hg19_uniform_prior |
|---|
| 81 | 0.218756601 | 0.036757495 | 0.4007557 | taca2.spliced.exon.3SS.hg19_uniform_prior |
|---|
| 9 | 0.217773464 | 0.017781764 | 0.4177652 | taca2.spliced.exon.5SS.hg19_uniform_prior |
|---|
RR of other annotations (separately)
https://yfu1116.github.io/project/0907_tadaA_res_modify/
joint estimation
1
| readRDS(paste0("/storage11_7T/fuy/TADA-A/annotation/results/",Sys.Date(),"_wes_all_joint_rr.rds"))
|
A data.frame: 18 × 4
| logRR | lower_bound | upper_bound | annota |
|---|
| <dbl> | <dbl> | <dbl> | <chr> |
|---|
| 0.90669919 | 0.60757718 | 1.2058212 | coding_constraint_regions_gt90 |
| -0.12910886 | -0.46264878 | 0.2044311 | ago_adult_brain.BA4.hg19 |
| 0.13822542 | -0.03550283 | 0.3119537 | alt3.spliced.exon.3SS.hg19 |
| 0.17572578 | 0.02751225 | 0.3239393 | alt3.spliced.exon.5SS.hg19 |
| -0.54716412 | -2.66639446 | 1.5720662 | alt5.spliced.exon.5SS.hg19 |
| 0.16053573 | 0.01180969 | 0.3092618 | iret.spliced.exon.3SS.hg19 |
| -0.03509237 | -0.40469967 | 0.3345149 | iret.spliced.exon.5SS.hg19 |
| -0.46034350 | NaN | NaN | mutx.spliced.exon.3SS.hg19 |
| 0.25686433 | 0.14773656 | 0.3659921 | SS5.constitutive_genome_ensembl.with.CLIP.genes.hg19 |
| 0.09324641 | -0.07820080 | 0.2646936 | taca2.spliced.exon.3SS.hg19 |
| -2.13668135 | NaN | NaN | taca2.spliced.exon.5SS.hg19 |
| 0.44380200 | -1.74845605 | 2.6360600 | gnomad.v2.1.1.all_lofs_snv |
| -0.31862933 | NaN | NaN | pLI_nlt_995_gnomad.v2.1.1.all_lofs_snv |
| 0.25858044 | -0.43798588 | 0.9551468 | annovar_all_lof |
| 0.59323606 | 0.30709175 | 0.8793804 | MVP_all_rare_missense_pathogen_gt_75 |
| -0.02275405 | -0.35847822 | 0.3129701 | primateAI_exome_mutation_pathogen_gt_80 |
| 0.96342266 | 0.68170418 | 1.2451411 | spidex_public_noncommercial_v1_0.tab_lower10pct |
| 0.68515719 | 0.30939716 | 1.0609172 | MPC_gt2 |
risk genes
A data.table: 19 × 9
| genename | logBF_coding | logBF_additional | logBF_all | BF_coding | BF_additional | BF_all | FDR_prior | FDR_all |
|---|
| <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> |
|---|
| SCN2A | 23.819414 | 0 | 23.819414 | 22112608564.43199 | 1 | 22112608564.43199 | 0.94 | 0.0000000007084948 |
| CHD8 | 15.006890 | 0 | 15.006890 | 3291618.50992 | 1 | 3291618.50992 | 0.94 | 0.0000023801245722 |
| SLC6A1 | 14.514623 | 0 | 14.514623 | 2011965.78798 | 1 | 2011965.78798 | 0.94 | 0.0000041823115228 |
| FOXP1 | 9.285647 | 0 | 9.285647 | 10782.15054 | 1 | 10782.15054 | 0.94 | 0.0003658643656144 |
| GRIN2B | 7.512955 | 0 | 7.512955 | 1831.61842 | 1 | 1831.61842 | 0.94 | 0.0019888743656405 |
| SYNGAP1 | 7.364811 | 0 | 7.364811 | 1579.41723 | 1 | 1579.41723 | 0.94 | 0.0032943694530575 |
| CHD2 | 5.902394 | 0 | 5.902394 | 365.91224 | 1 | 365.91224 | 0.94 | 0.0086890989094275 |
| PRKAR1B | 5.272396 | 0 | 5.272396 | 194.88234 | 1 | 194.88234 | 0.94 | 0.0169040424423985 |
| WBSCR17 | 5.053927 | 0 | 5.053927 | 156.63643 | 1 | 156.63643 | 0.94 | 0.0251285982154869 |
| SETD5 | 5.016052 | 0 | 5.016052 | 150.81467 | 1 | 150.81467 | 0.94 | 0.0320262023969106 |
| KCNMA1 | 4.768129 | 0 | 4.768129 | 117.69887 | 1 | 117.69887 | 0.94 | 0.0397939684644295 |
| RHOBTB2 | 4.755046 | 0 | 4.755046 | 116.16895 | 1 | 116.16895 | 0.94 | 0.0463807092823956 |
| LRRC43 | 4.716614 | 0 | 4.716614 | 111.78910 | 1 | 111.78910 | 0.94 | 0.0522682284941430 |
| UGT1A1 | 4.551697 | 0 | 4.551697 | 94.79317 | 1 | 94.79317 | 0.94 | 0.0586655933901719 |
| IQSEC2 | 4.544424 | 0 | 4.544424 | 94.10621 | 1 | 94.10621 | 0.94 | 0.0642691483797639 |
| TRIP12 | 4.226253 | 0 | 4.226253 | 68.46022 | 1 | 68.46022 | 0.94 | 0.0718914906632107 |
| PAX8 | 4.225071 | 0 | 4.225071 | 68.37937 | 1 | 68.37937 | 0.94 | 0.0786276254360439 |
| FBN1 | 4.093336 | 0 | 4.093336 | 59.93949 | 1 | 59.93949 | 0.94 | 0.0857713213511628 |
| LRP10 | 4.013766 | 0 | 4.013766 | 55.35496 | 1 | 55.35496 | 0.94 | 0.0928670461408945 |
risk genes not found in that WES study
1
| readRDS(paste0("/storage11_7T/fuy/TADA-A/annotation/results/",Sys.Date(),"_wes_all_g_BF2_noval.rds"))
|
A data.table: 9 × 9
| genename | logBF_noncoding | logBF_coding | logBF_all | BF_noncoding | BF_coding | BF_all | FDR_coding | FDR_all |
|---|
| <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> |
|---|
| PRKAR1B | 5.272396 | 0 | 5.272396 | 194.88234 | 1 | 194.88234 | 0.94 | 0.01690404 |
| WBSCR17 | 5.053927 | 0 | 5.053927 | 156.63643 | 1 | 156.63643 | 0.94 | 0.02512860 |
| RHOBTB2 | 4.755046 | 0 | 4.755046 | 116.16895 | 1 | 116.16895 | 0.94 | 0.04638071 |
| LRRC43 | 4.716614 | 0 | 4.716614 | 111.78910 | 1 | 111.78910 | 0.94 | 0.05226823 |
| UGT1A1 | 4.551697 | 0 | 4.551697 | 94.79317 | 1 | 94.79317 | 0.94 | 0.05866559 |
| IQSEC2 | 4.544424 | 0 | 4.544424 | 94.10621 | 1 | 94.10621 | 0.94 | 0.06426915 |
| PAX8 | 4.225071 | 0 | 4.225071 | 68.37937 | 1 | 68.37937 | 0.94 | 0.07862763 |
| FBN1 | 4.093336 | 0 | 4.093336 | 59.93949 | 1 | 59.93949 | 0.94 | 0.08577132 |
| LRP10 | 4.013766 | 0 | 4.013766 | 55.35496 | 1 | 55.35496 | 0.94 | 0.09286705 |
