Added new code 'ribo-biotin.Rmd'

ComputationalProteomicsUnit · Oct 15, 2019 · de7cb69 · de7cb69
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diff --git a/...07_Output/Ab-APEX_IUPred-L_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf b/...07_Output/Ab-APEX_IUPred-L_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf
diff --git a/...put/Ab-APEX_VSL2b.IUPred-L_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf b/...put/Ab-APEX_VSL2b.IUPred-L_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf
diff --git a/...08-07_Output/Ab-APEX_VSL2b_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf b/...08-07_Output/Ab-APEX_VSL2b_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf
diff --git a/...Output/Ab-APEX_all-callers_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf b/...Output/Ab-APEX_all-callers_Distribution-of-PTMs-in.out.of.IDRs-by-study-and-abundance.pdf
diff --git a/2018-08-07_Output/Binomial-test-values-by-quartile.txt b/2018-08-07_Output/Binomial-test-values-by-quartile.txt
@@ -0,0 +1,81 @@
+study	caller	quantile	idrY	allY	in	out	tot.biot.idr	tot.biot	in	out	V12
+Ab-APEX	IUPred-L	Q4	93	1789	5.2	94.8	42	307	13.68	86.32	1.36223932698783e-08
+Ab-APEX	IUPred-L	Q5	291	3027	9.61	90.39	36	355	10.14	89.86	0.393685156500442
+Ab-APEX	IUPred-L	Q3	22	767	2.87	97.13	18	164	10.98	89.02	1.38748803864719e-06
+Ab-APEX	IUPred-L	Q2	9	264	3.41	96.59	10	89	11.24	88.76	0.000923385192149869
+Ab-APEX	IUPred-L	Q1	1	25	4	96	0	8	0	100	1
+BioSITe	IUPred-L	Q4	797	2763	28.85	71.15	130	408	31.86	68.14	0.099239983557981
+BioSITe	IUPred-L	Q5	1889	8583	22.01	77.99	329	714	46.08	53.92	6.03667661099087e-46
+BioSITe	IUPred-L	Q3	355	1129	31.44	68.56	61	210	29.05	70.95	0.793644456049105
+BioSITe	IUPred-L	Q2	75	290	25.86	74.14	23	89	25.84	74.16	0.542107275494004
+BioSITe	IUPred-L	Q1	2	25	8	92	2	7	28.57	71.43	0.10259459801088
+DiDBIT	IUPred-L	Q4	4410	18925	23.3	76.7	470	2475	18.99	81.01	0.999999908496871
+DiDBIT	IUPred-L	Q5	10731	75616	14.19	85.81	1654	5778	28.63	71.37	1.40014828597966e-176
+DiDBIT	IUPred-L	Q3	2292	9924	23.1	76.9	371	1719	21.58	78.42	0.936278235434567
+DiDBIT	IUPred-L	Q2	850	3863	22	78	228	834	27.34	72.66	0.000165427631597839
+DiDBIT	IUPred-L	Q1	212	956	22.18	77.82	64	172	37.21	62.79	5.64008636604876e-06
+SpotBioID	IUPred-L	Q4	876	3483	25.15	74.85	74	171	43.27	56.73	1.86267073108771e-07
+SpotBioID	IUPred-L	Q5	4128	28869	14.3	85.7	394	616	63.96	36.04	5.5881962761121e-175
+SpotBioID	IUPred-L	Q3	295	1406	20.98	79.02	56	107	52.34	47.66	9.32192202634258e-13
+SpotBioID	IUPred-L	Q2	66	412	16.02	83.98	33	54	61.11	38.89	8.53620905831245e-14
+SpotBioID	IUPred-L	Q1	1	24	4.17	95.83	1	5	20	80	0.191680657029642
+Ab-APEX	VSL2b	Q4	204	1789	11.4	88.6	83	307	27.04	72.96	4.53937984374217e-14
+Ab-APEX	VSL2b	Q5	606	3027	20.02	79.98	71	355	20	80	0.524883742677512
+Ab-APEX	VSL2b	Q3	44	767	5.74	94.26	56	164	34.15	65.85	2.04044120176689e-28
+Ab-APEX	VSL2b	Q2	17	264	6.44	93.56	32	89	35.96	64.04	3.01804974049753e-16
+Ab-APEX	VSL2b	Q1	2	25	8	92	3	8	37.5	62.5	0.0211004858302464
+BioSITe	VSL2b	Q4	1318	2763	47.7	52.3	197	408	48.28	51.72	0.425939705283733
+BioSITe	VSL2b	Q5	2778	8583	32.37	67.63	423	714	59.24	40.76	4.04904043151696e-49
+BioSITe	VSL2b	Q3	571	1129	50.58	49.42	104	210	49.52	50.48	0.645800390607167
+BioSITe	VSL2b	Q2	131	290	45.17	54.83	39	89	43.82	56.18	0.640399585586985
+BioSITe	VSL2b	Q1	2	25	8	92	3	7	42.86	57.14	0.0140140412928
+DiDBIT	VSL2b	Q4	7987	18925	42.2	57.8	1145	2475	46.26	53.74	2.51402263136215e-05
+DiDBIT	VSL2b	Q5	16976	75616	22.45	77.55	3197	5778	55.33	44.67	0
+DiDBIT	VSL2b	Q3	4495	9924	45.29	54.71	898	1719	52.24	47.76	4.58692806995159e-09
+DiDBIT	VSL2b	Q2	1597	3863	41.34	58.66	484	834	58.03	41.97	2.30193430977359e-22
+DiDBIT	VSL2b	Q1	357	956	37.34	62.66	112	172	65.12	34.88	1.5217474109728e-13
+SpotBioID	VSL2b	Q4	1248	3483	35.83	64.17	135	171	78.95	21.05	1.1254992636154e-30
+SpotBioID	VSL2b	Q5	5517	28869	19.11	80.89	511	616	82.95	17.05	7.3140493018795e-257
+SpotBioID	VSL2b	Q3	452	1406	32.15	67.85	79	107	73.83	26.17	1.2014532074501e-18
+SpotBioID	VSL2b	Q2	95	412	23.06	76.94	47	54	87.04	12.96	3.33779125905731e-23
+SpotBioID	VSL2b	Q1	4	24	16.67	83.33	3	5	60	40	0.0354938271604938
+Ab-APEX	VSL2b.IUPred-L	Q4	208	1789	11.63	88.37	85	307	27.69	72.31	1.55580548399806e-14
+Ab-APEX	VSL2b.IUPred-L	Q5	627	3027	20.71	79.29	75	355	21.13	78.87	0.444656460673224
+Ab-APEX	VSL2b.IUPred-L	Q3	47	767	6.13	93.87	57	164	34.76	65.24	6.51093323295931e-28
+Ab-APEX	VSL2b.IUPred-L	Q2	17	264	6.44	93.56	33	89	37.08	62.92	3.56587750139722e-17
+Ab-APEX	VSL2b.IUPred-L	Q1	2	25	8	92	3	8	37.5	62.5	0.0211004858302464
+BioSITe	VSL2b.IUPred-L	Q4	1370	2763	49.58	50.42	201	408	49.26	50.74	0.570735473998289
+BioSITe	VSL2b.IUPred-L	Q5	2872	8583	33.46	66.54	440	714	61.62	38.38	2.81070817310981e-53
+BioSITe	VSL2b.IUPred-L	Q3	591	1129	52.35	47.65	106	210	50.48	49.52	0.729889617010176
+BioSITe	VSL2b.IUPred-L	Q2	135	290	46.55	53.45	40	89	44.94	55.06	0.658357173895453
+BioSITe	VSL2b.IUPred-L	Q1	3	25	12	88	4	7	57.14	42.86	0.0053692637184
+DiDBIT	VSL2b.IUPred-L	Q4	8195	18925	43.3	56.7	1160	2475	46.87	53.13	0.000191758715039099
+DiDBIT	VSL2b.IUPred-L	Q5	17449	75616	23.08	76.92	3250	5778	56.25	43.75	0
+DiDBIT	VSL2b.IUPred-L	Q3	4594	9924	46.29	53.71	910	1719	52.94	47.06	1.98373471258611e-08
+DiDBIT	VSL2b.IUPred-L	Q2	1643	3863	42.53	57.47	490	834	58.75	41.25	3.59672576763849e-21
+DiDBIT	VSL2b.IUPred-L	Q1	371	956	38.81	61.19	112	172	65.12	34.88	2.81682580379354e-12
+SpotBioID	VSL2b.IUPred-L	Q4	1294	3483	37.15	62.85	137	171	80.12	19.88	1.66242436192058e-30
+SpotBioID	VSL2b.IUPred-L	Q5	5681	28869	19.68	80.32	529	616	85.88	14.12	7.24043804038165e-275
+SpotBioID	VSL2b.IUPred-L	Q3	457	1406	32.5	67.5	81	107	75.7	24.3	6.58895724919885e-20
+SpotBioID	VSL2b.IUPred-L	Q2	95	412	23.06	76.94	47	54	87.04	12.96	3.33779125905731e-23
+SpotBioID	VSL2b.IUPred-L	Q1	4	24	16.67	83.33	3	5	60	40	0.0354938271604938
+Ab-APEX	all-callers	Q4	71	1789	3.97	96.03	33	307	10.75	89.25	2.95984294960195e-07
+Ab-APEX	all-callers	Q5	188	3027	6.21	93.79	22	355	6.2	93.8	0.535296977544951
+Ab-APEX	all-callers	Q3	15	767	1.96	98.04	13	164	7.93	92.07	2.40617225061569e-05
+Ab-APEX	all-callers	Q2	5	264	1.89	98.11	10	89	11.24	88.76	7.72202943068043e-06
+Ab-APEX	all-callers	Q1	1	25	4	96	0	8	0	100	1
+BioSITe	all-callers	Q4	629	2763	22.77	77.23	114	408	27.94	72.06	0.00848878048295264
+BioSITe	all-callers	Q5	1488	8583	17.34	82.66	251	714	35.15	64.85	2.88193841574907e-30
+BioSITe	all-callers	Q3	285	1129	25.24	74.76	49	210	23.33	76.67	0.761191023565066
+BioSITe	all-callers	Q2	65	290	22.41	77.59	21	89	23.6	76.4	0.435212136294268
+BioSITe	all-callers	Q1	1	25	4	96	0	7	0	100	1
+DiDBIT	all-callers	Q4	3544	18925	18.73	81.27	348	2475	14.06	85.94	0.999999999695577
+DiDBIT	all-callers	Q5	8509	75616	11.25	88.75	1141	5778	19.75	80.25	2.31055139824558e-78
+DiDBIT	all-callers	Q3	1865	9924	18.79	81.21	298	1719	17.34	82.66	0.943790450839468
+DiDBIT	all-callers	Q2	747	3863	19.34	80.66	195	834	23.38	76.62	0.00216993342182767
+DiDBIT	all-callers	Q1	196	956	20.5	79.5	66	172	38.37	61.63	5.93763312105052e-08
+SpotBioID	all-callers	Q4	721	3483	20.7	79.3	56	171	32.75	67.25	0.000158364270672343
+SpotBioID	all-callers	Q5	3303	28869	11.44	88.56	278	616	45.13	54.87	1.46872474901785e-97
+SpotBioID	all-callers	Q3	254	1406	18.07	81.93	48	107	44.86	55.14	1.61453703326882e-10
+SpotBioID	all-callers	Q2	57	412	13.83	86.17	30	54	55.56	44.44	7.60797675487101e-13
+SpotBioID	all-callers	Q1	0	24	0	100	1	5	20	80	0
diff --git a/2018-08-07_Output/Binomial-test-values-by-quartile.xlsx b/2018-08-07_Output/Binomial-test-values-by-quartile.xlsx