2021-04-19-tadaA-report

gama and the number of risk genes

  • fixed pi (pi=0.05)
  • estimated pi
In [3]:
readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/indel_rate/all_gm_n_gene.rds")
A data.frame: 3 × 4
gamalog_gmn_risk_gannota
<dbl><dbl><dbl><chr>
3.2575651.18098097estimate_pi_annota1-16_indel
4.6013781.52635672estimate_pi_annota_MPC_PTV_indel
7.2553371.98173785fixed_pi_1-16annota_indel

functional enrichment of novel genes

  • estimated pi
  • fixed pi

The enrichment of novel genes from new method is always higher than that from the old one.

In [2]:
readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/indel_rate/genelist_EA_rest_gene_16annota_estimate_fixed_pi.rds")
A data.frame: 16 × 5
Genesetesti_enrichesti_pvalfixed_enrichfixed_pval
<fct><dbl><dbl><dbl><dbl>
haploinsufficiency/Petrovski_plosgen_haploinsufficiency_including_all_without_ncscore_genelist.txt 5.99860.000000 3.94640.000120
brainspan/top5%_brainspan_exp.gene.lst 1.03180.583871 1.93450.200930
RVIS/Petrovski_plosgen_RVIS_score_top5_pct_genelist.txt 7.03010.000000 4.73180.000537
160210_GO_brain_genes.txt 2.42080.000343 2.26950.003531
AutismKB_genelist.txt 10.40360.002975 8.66960.022209
Olfactory_genelist.txt 0.00001.000000 0.00001.000000
sfrai/sfrai_genes_high_confidence_genelist_new_170717.txt 19.86140.04918624.82670.039538
sfrai/sfrai_curated_ASD_associated_genelist.txt 6.81770.000000 6.19790.000030
Darnell_Cell_2011_FMRP_targets_genelist.txt 6.37460.000001 4.34630.002189
DAWN_new_q0.05_genelist.txt 5.13300.000130 7.21830.000002
Kenny_MP_2014_brain_functional_genelist.txt 8.60990.001164 5.38120.053022
Irimia_cell_2014_neuron_specific_alternative_splicing_genelist.txt 2.90910.001647 2.18180.052220
samocha_NG_2014_top5_percent_genelist.txt 5.74090.000019 2.39210.128882
RBPDB.gene.lst 0.00001.000000 0.00001.000000
Xin_asd_gene_qvalue_0.1/Xin_ASD_gene_qvalue_0_1.genelist 20.48200.00042025.60250.000215
cell_q_ls03.gene.lst 28.06100.00000020.04360.000000