2021-05-20-fix-pi-VS-estim-pi-effect-size-num-enrich

effect size

add a new annotation mixture of spidex_low3% and merged spliceai, without PTVs, and remove the original ones.

the difference of effect size between fix pi and estimate pi is small.

1	readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-05-21_selected14_fix_pi_estim_pi_joint_sep_rr.rds")

A data.frame: 14 × 6
	fix_pi0.05_joint_logRR	estim_pi_joint_logRR, pi = 0.12	annota	separate_logRR	upper_bound	lower_bound
	<dbl>	<dbl>	<chr>	<dbl>	<dbl>	<dbl>
1	1.1100917	0.7600744	hnRNPL binding regions	1.599488	3.083753	0.1152234
2	0.3510368	0.2743483	coding constraint >= 90	1.897444	2.103377	1.6915119
3	0.8990006	0.5676109	mixture of spidex_low3% and merged spliceai, without PTVs	1.350766	2.051145	0.6503864
4	1.0255459	0.8607562	dbSNP.RBP-Var: likely to affcted RNA-bind, RNA 2nd structure	1.844203	2.278540	1.4098657
5	0.8414096	0.6799831	RNA modifications, including m6a, m1A, m5C, and etc.(filter_low_RMVar_hb)	1.312018	1.645988	0.9780486
6	0.5513090	0.5873327	deepsea: mix ago_adult_brain.BA4 & ago_adult_brain.Cingulate.gyrus	2.483918	2.903837	2.0639991
7	0.1064622	0.5020994	deepsea: mix elavl_Adult_brain.all_human_samples & elavl_Adult_brain.BA9_Alzheimer & elavl_Adult_brain.BA9	2.592861	3.006368	2.1793531
8	0.2703671	0.2492257	1<= mpc score < 2	1.621601	1.835855	1.4073458
9	0.7994336	0.7232636	mpc score >= 2	2.321405	2.547951	2.0948598
10	0.9720178	0.7773866	interaction-disrupting: mutations annotated as interface residues and probably damaging by PolyPhen-2	2.600493	2.828070	2.3729150
11	1.0088334	0.7638980	pathogenic missense: primateAI_MVP_mix	1.757185	1.892405	1.6219658
12	1.9444620	1.3522520	ptv in [0,0.5)	2.081598	2.557930	1.6052671
13	1.4360216	1.1693845	ptv in [0.5,0.995)	2.209710	2.964529	1.4548916
14	3.1558238	2.7545241	ptv in [0.995,1)	3.493791	3.759486	3.2280951

genes identified

the number of risk genes identified via estimate pi is more than that identified via fix pi

risk genes identified via estimate pi have higher enrichment in ASD-associated genesets.

1 2	data.frame(pi=c("fixed","estimated") ,num_gene_identified = c(66,81)) mg

A data.frame: 2 × 2
pi	num_gene_identified
<fct>	<dbl>
fixed	66
estimated	81

A data.frame: 13 × 9
	Geneset	fixed:enrich	fixed:pVal	fixed: gene num	fixed:in geneset	estim:enrich	estim:pVal	estim:gene num	estim:in geneset
	<chr>	<dbl>	<dbl>	<int>	<int>	<dbl>	<dbl>	<int>	<int>
1	haploinsufficiency_including_all_without_ncscore	4.2095	0.000000	66	22	4.5214	0.000000	81	29
2	brainspan/top5%_brainspan_exp.gene.lst	1.5633	0.215187	66	5	2.2928	0.016285	81	9
3	RVIS/Petrovski_plosgen_RVIS_score_top5_pct	6.5549	0.000000	66	20	6.9433	0.000000	81	26
4	160210_GO_brain_genes.txt	2.8426	0.000000	66	31	2.7645	0.000000	81	37
5	AutismKB	29.4242	0.000000	66	14	29.1129	0.000000	81	17
6	Olfactory	0.0000	1.000000	66	0	0.0000	1.000000	81	0
7	sfrai_genes_high_confidence_170717	180.5579	0.000000	66	15	176.5455	0.000000	81	18
8	sfrai/sfrai_curated_ASD_associated	13.5226	0.000000	66	36	12.5488	0.000000	81	41
9	Darnell_Cell_2011_FMRP_targets	9.1317	0.000000	66	26	10.3024	0.000000	81	36
10	DAWN_new_q0.05	14.3881	0.000000	66	37	13.9416	0.000000	81	44
11	Kenny_MP_2014_brain_functional	11.7407	0.000000	66	9	12.7553	0.000000	81	12
12	Irimia_cell_2014_neuron_specific_alternative_splicing	1.7631	0.054322	66	10	2.0112	0.008707	81	14
13	samocha_NG_2014_top5_percent	8.1185	0.000000	66	21	9.1351	0.000000	81	29

# fix = readRDS(paste0("/storage11_7T/fuy/TADA-A/cell_WES/DNM/",Sys.Date(),"_selected14_fix_pi_risk_genes.rds"))
# estim = readRDS(paste0("/storage11_7T/fuy/TADA-A/cell_WES/DNM/",Sys.Date(),"_selected14_estim_pi_risk_genes.rds"))
# mg = cbind(df.fix[,1:5],df.estim[,2:5])[1:13,]
# colnames(mg) = c("Geneset","fixed:enrich","fixed:pVal","fixed: gene num","fixed:in geneset",
#                 "estim:enrich","estim:pVal","estim:gene num","estim:in geneset")
# mg$Geneset = as.character(mg$Geneset)
# mg$Geneset[1]="haploinsufficiency_including_all_without_ncscore_genelist.txt"
# mg$Geneset = gsub("_genelist.txt", "", mg$Geneset)
# mg$Geneset[7] = "sfrai_genes_high_confidence_170717"
# saveRDS(mg,"/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-05-21_selected14_fix_vs_estim_pi_EA.rds")