Added network functionality; updated test data

loosolab · Aug 28, 2019 · f9910a4 · f9910a4
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commit f9910a4
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Showing 109 changed files with 51,301 additions and 30,227 deletions.
diff --git a/test_data/BATFJUN_Bcell_bound.bed b/test_data/BATFJUN_Bcell_bound.bed
diff --git a/test_data/BATFJUN_Bcell_unbound.bed b/test_data/BATFJUN_Bcell_unbound.bed
diff --git a/test_data/BATFJUN_Tcell_bound.bed b/test_data/BATFJUN_Tcell_bound.bed
diff --git a/test_data/BATFJUN_Tcell_unbound.bed b/test_data/BATFJUN_Tcell_unbound.bed
diff --git a/test_data/BATFJUN_all.bed b/test_data/BATFJUN_all.bed
diff --git a/test_data/Bcell_bias.bw b/test_data/Bcell_bias.bw
diff --git a/test_data/Bcell_corrected.bw b/test_data/Bcell_corrected.bw
diff --git a/test_data/Bcell_expected.bw b/test_data/Bcell_expected.bw
diff --git a/test_data/Bcell_footprints.bw b/test_data/Bcell_footprints.bw
diff --git a/test_data/Bcell_uncorrected.bw b/test_data/Bcell_uncorrected.bw
diff --git a/test_data/IRF1_all.bed b/test_data/IRF1_all.bed
diff --git a/test_data/IRF1_bound.bed b/test_data/IRF1_bound.bed
diff --git a/test_data/IRF1_unbound.bed b/test_data/IRF1_unbound.bed
diff --git a/test_data/Tcell_corrected.bw b/test_data/Tcell_corrected.bw
diff --git a/test_data/Tcell_footprints.bw b/test_data/Tcell_footprints.bw
diff --git a/test_data/annotated_peaks.bed b/test_data/annotated_peaks.bed
diff --git a/test_data/annotated_peaks_header.txt b/test_data/annotated_peaks_header.txt
@@ -1,13 +1 @@
-peak_chr
-peak_start
-peak_end
-peak_id
-feature
-feat_start
-feat_end
-feat_strand
-feat_anchor
-distance
-gene_biotype
-gene_id
-gene_name
+peak_chr	peak_start	peak_end	peak_id	feature	feat_start	feat_end	feat_strand	feat_anchor	distance	relative_location	gene_biotype	gene_id	gene_name	name
diff --git a/test_data/annotated_tfbs/ATF7_MA0834.1_Bcell_bound.bed b/test_data/annotated_tfbs/ATF7_MA0834.1_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/Ar_MA0007.3_Bcell_bound.bed b/test_data/annotated_tfbs/Ar_MA0007.3_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/Arnt_MA0004.1_Bcell_bound.bed b/test_data/annotated_tfbs/Arnt_MA0004.1_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/BACH2_MA1101.1_Bcell_bound.bed b/test_data/annotated_tfbs/BACH2_MA1101.1_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/BATFJUN_MA0462.1_Bcell_bound.bed b/test_data/annotated_tfbs/BATFJUN_MA0462.1_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/BHLHE40_MA0464.2_Bcell_bound.bed b/test_data/annotated_tfbs/BHLHE40_MA0464.2_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/Bach1Mafk_MA0591.1_Bcell_bound.bed b/test_data/annotated_tfbs/Bach1Mafk_MA0591.1_Bcell_bound.bed
diff --git a/test_data/annotated_tfbs/CEBPB_MA0466.2_Bcell_bound.bed b/test_data/annotated_tfbs/CEBPB_MA0466.2_Bcell_bound.bed
@@ -0,0 +1,77 @@
+chr4	699527	699537	CEBPB_MA0466.2	10.67825	-	chr4	699408	699758	Bcell,Tcell	gene	705747	770640	+	start	6164	Upstream	protein_coding	ENSG00000185619	PCGF3	8.13701
+chr4	4689744	4689754	CEBPB_MA0466.2	8.08706	-	chr4	4689568	4690219	Bcell	gene	4542130	4710938	+	end	21045	PeakInsideFeature	antisense	ENSG00000247708	STX18-AS1	14.81069
+chr4	8159051	8159061	CEBPB_MA0466.2	8.50345	+	chr4	8158663	8159388	Bcell,Tcell	gene	7965309	8158832	-	start	193	OverlapStart	protein_coding	ENSG00000163995	ABLIM2	7.71347
+chr4	10006409	10006419	CEBPB_MA0466.2	7.64161	-	chr4	10006298	10006646	Bcell	gene	9771152	10054936	-	start	48464	PeakInsideFeature	protein_coding	ENSG00000109667	SLC2A9	10.52037
+chr4	10554882	10554892	CEBPB_MA0466.2	7.99524	+	chr4	10554681	10554961	Bcell,Tcell	gene	10486394	10684865	-	center	30808	PeakInsideFeature	protein_coding	ENSG00000109684	CLNK	8.63747
+chr4	14125516	14125526	CEBPB_MA0466.2	7.14982	-	chr4	14125375	14126047	Bcell	gene	14134935	14143592	+	start	9224	Upstream	lincRNA	ENSG00000251679	AC073848.1	11.57009
+chr4	23334105	23334115	CEBPB_MA0466.2	7.91235	-	chr4	23333645	23334665	Bcell,Tcell	gene	23234624	23285573	-	start	48582	Downstream	lincRNA	ENSG00000249547	AC092440.1	10.84564
+chr4	38820464	38820474	CEBPB_MA0466.2	8.22584	-	chr4	38820320	38820607	Bcell	gene	38790676	38856817	-	center	3283	PeakInsideFeature	protein_coding	ENSG00000174125	TLR1	7.84527
+chr4	39458961	39458971	CEBPB_MA0466.2	8.53149	-	chr4	39458226	39459542	Bcell,Tcell	gene	39452520	39458949	-	start	65	OverlapStart	protein_coding	ENSG00000163682	RPL9	10.87988
+chr4	40992208	40992218	CEBPB_MA0466.2	7.83515	-	chr4	40991874	40992542	Bcell	gene	40810026	41216714	-	center	21162	PeakInsideFeature	protein_coding	ENSG00000163697	APBB2	7.81756
+chr4	48036879	48036889	CEBPB_MA0466.2	8.73215	-	chr4	48036421	48037046	Bcell	gene	47914141	48040173	+	end	3440	PeakInsideFeature	protein_coding	ENSG00000163293	NIPAL1	11.56845
+chr4	64314658	64314668	CEBPB_MA0466.2	7.30689	-	chr4	64314552	64314752	Bcell	gene	64275256	64409468	-	center	27710	PeakInsideFeature	protein_coding	ENSG00000205678	TECRL	6.87674
+chr4	68350295	68350305	CEBPB_MA0466.2	8.73215	+	chr4	68349413	68350330	Bcell,Tcell	gene	68310386	68350089	-	start	218	OverlapStart	protein_coding	ENSG00000083896	YTHDC1	6.35211
+chr4	73536553	73536563	CEBPB_MA0466.2	8.33809	+	chr4	73535962	73536645	Bcell	gene	73543821	73544013	+	start	7518	Upstream	processed_pseudogene	ENSG00000249970	AC074250.1	8.14474
+chr4	74099374	74099384	CEBPB_MA0466.2	7.91235	-	chr4	74099143	74099472	Bcell	gene	74097034	74099293	-	start	14	OverlapStart	protein_coding	ENSG00000081041	CXCL2	6.20456
+chr4	75848533	75848543	CEBPB_MA0466.2	8.73215	+	chr4	75848132	75848603	Bcell	gene	75859863	75902571	-	end	11496	Upstream	protein_coding	ENSG00000156194	PPEF2	12.39782
+chr4	77158130	77158140	CEBPB_MA0466.2	8.51955	-	chr4	77157931	77158472	Bcell	gene	77157150	77433388	+	start	1051	PeakInsideFeature	protein_coding	ENSG00000138764	CCNG2	10.8182
+chr4	79224423	79224433	CEBPB_MA0466.2	8.21873	-	chr4	79224124	79225257	Bcell	gene	78971747	79308798	+	end	84108	PeakInsideFeature	antisense	ENSG00000249307	LINC01088	7.92095
+chr4	81406019	81406029	CEBPB_MA0466.2	8.91361	+	chr4	81405831	81406320	Bcell,Tcell	gene	81426392	82044244	-	end	20317	Upstream	protein_coding	ENSG00000138670	RASGEF1B	8.87264
+chr4	82462512	82462522	CEBPB_MA0466.2	7.83515	-	chr4	82462436	82462784	Bcell,Tcell	gene	82430561	82461091	+	end	1519	Downstream	protein_coding	ENSG00000145293	ENOPH1	7.04113
+chr4	85475169	85475179	CEBPB_MA0466.2	8.42981	+	chr4	85474814	85475541	Bcell	gene	85475113	86002670	+	start	64	OverlapStart	protein_coding	ENSG00000138639	ARHGAP24	7.87662
+chr4	86441494	86441504	CEBPB_MA0466.2	7.14982	+	chr4	86441137	86441776	Bcell	gene	85990006	86594625	-	center	149141	PeakInsideFeature	protein_coding	ENSG00000109339	MAPK10	7.16552
+chr4	87209909	87209919	CEBPB_MA0466.2	8.33809	+	chr4	87209632	87210092	Bcell,Tcell	gene	87160102	87240314	-	center	9654	PeakInsideFeature	protein_coding	ENSG00000145332	KLHL8	16.12933
+chr4	87391248	87391258	CEBPB_MA0466.2	8.50345	+	chr4	87391027	87391628	Bcell,Tcell	gene	87336609	87391386	-	start	59	OverlapStart	protein_coding	ENSG00000198189	HSD17B11	26.53812
+chr4	87677884	87677894	CEBPB_MA0466.2	8.31179	-	chr4	87677743	87678107	Bcell	gene	87568034	87733956	-	center	26930	PeakInsideFeature	antisense	ENSG00000249001	AC093895.1	7.51053
+chr4	88803754	88803764	CEBPB_MA0466.2	8.26039	+	chr4	88803619	88803912	Bcell	gene	88725954	89111398	-	end	77811	PeakInsideFeature	protein_coding	ENSG00000138640	FAM13A	7.91426
+chr4	90118693	90118703	CEBPB_MA0466.2	10.05947	+	chr4	90118632	90119033	Bcell	gene	90127534	91601913	+	start	8702	Upstream	protein_coding	ENSG00000184305	CCSER1	6.86862
+chr4	90128776	90128786	CEBPB_MA0466.2	7.14271	-	chr4	90128002	90128840	Bcell	gene	90127534	91601913	+	start	887	PeakInsideFeature	protein_coding	ENSG00000184305	CCSER1	7.58329
+chr4	94127953	94127963	CEBPB_MA0466.2	7.60706	+	chr4	94127789	94128039	Bcell	gene	94117791	94207556	-	end	10123	PeakInsideFeature	lincRNA	ENSG00000246541	AC096746.1	12.64095
+chr4	94207599	94207609	CEBPB_MA0466.2	8.52438	-	chr4	94207398	94208313	Bcell,Tcell	gene	94207610	94291292	+	start	245	OverlapStart	protein_coding	ENSG00000163104	SMARCAD1	26.10837
+chr4	98203741	98203751	CEBPB_MA0466.2	8.08706	-	chr4	98203385	98204567	Bcell,Tcell	gene	98251687	98261630	-	end	47711	Upstream	antisense	ENSG00000214559	AC019077.1	8.50061
+chr4	98447255	98447265	CEBPB_MA0466.2	8.33809	+	chr4	98446500	98447581	Bcell,Tcell	gene	98261383	98443861	+	end	3179	Downstream	protein_coding	ENSG00000138698	RAP1GDS1	24.92239
+chr4	99088250	99088260	CEBPB_MA0466.2	8.25328	+	chr4	99088198	99089608	Bcell,Tcell	gene	99070977	99088801	-	start	102	OverlapStart	protein_coding	ENSG00000197894	ADH5	6.33953
+chr4	101346594	101346604	CEBPB_MA0466.2	8.51955	+	chr4	101345983	101348277	Bcell,Tcell	gene	101023408	101348278	-	start	1148	PeakInsideFeature	protein_coding	ENSG00000138814	PPP3CA	9.88062
+chr4	103009298	103009308	CEBPB_MA0466.2	8.51244	-	chr4	103009177	103009469	Bcell,Tcell	gene	102885047	103019739	-	start	10416	PeakInsideFeature	protein_coding	ENSG00000164037	SLC9B1	9.37133
+chr4	103019655	103019665	CEBPB_MA0466.2	10.05947	-	chr4	103019465	103020231	Bcell,Tcell	gene	102885047	103019739	-	start	109	OverlapStart	protein_coding	ENSG00000164037	SLC9B1	34.3618
+chr4	104966797	104966807	CEBPB_MA0466.2	8.51244	+	chr4	104966680	104967292	Bcell,Tcell	gene	104653873	104966793	-	start	193	OverlapStart	lincRNA	ENSG00000248242	AC004053.1	13.99984
+chr4	108620511	108620521	CEBPB_MA0466.2	7.9056	+	chr4	108620206	108621021	Bcell,Tcell	gene	108620565	108630412	+	start	48	OverlapStart	protein_coding	ENSG00000109475	RPL34	14.86447
+chr4	110315680	110315690	CEBPB_MA0466.2	8.29482	-	chr4	110315535	110315735	Bcell	gene	110291643	110293573	+	end	22062	Downstream	processed_pseudogene	ENSG00000250304	ZBED1P1	12.2548
+chr4	111642179	111642189	CEBPB_MA0466.2	8.9065	+	chr4	111642117	111642437	Bcell	gene	111640494	111648808	+	start	1783	PeakInsideFeature	lincRNA	ENSG00000248656	AC083795.2	6.00206
+chr4	112279722	112279732	CEBPB_MA0466.2	8.73215	+	chr4	112279103	112279836	Bcell	gene	112285508	112442620	+	start	6039	Upstream	protein_coding	ENSG00000073331	ALPK1	28.21639
+chr4	112297289	112297299	CEBPB_MA0466.2	8.70584	+	chr4	112296915	112297495	Bcell,Tcell	gene	112285508	112442620	+	start	11697	PeakInsideFeature	protein_coding	ENSG00000073331	ALPK1	9.94431
+chr4	112312765	112312775	CEBPB_MA0466.2	8.25328	+	chr4	112312232	112313099	Bcell	gene	112285508	112442620	+	start	27157	PeakInsideFeature	protein_coding	ENSG00000073331	ALPK1	14.8194
+chr4	113636545	113636555	CEBPB_MA0466.2	8.08706	+	chr4	113636526	113637391	Bcell,Tcell	gene	113451031	113761927	-	center	30479	PeakInsideFeature	protein_coding	ENSG00000145349	CAMK2D	7.23523
+chr4	113761442	113761452	CEBPB_MA0466.2	8.72106	-	chr4	113761070	113762955	Bcell,Tcell	gene	113451031	113761927	-	start	85	OverlapStart	protein_coding	ENSG00000145349	CAMK2D	7.94219
+chr4	118592006	118592016	CEBPB_MA0466.2	8.72504	+	chr4	118591404	118592094	Bcell,Tcell	gene	118591772	118633729	+	start	23	OverlapStart	transcribed_unprocessed_pseudogene	ENSG00000260404	AC110079.1	10.49997
+chr4	118685283	118685293	CEBPB_MA0466.2	8.33098	+	chr4	118685176	118685792	Bcell,Tcell	gene	118685367	118715433	+	start	117	OverlapStart	protein_coding	ENSG00000145388	METTL14	20.39828
+chr4	119454380	119454390	CEBPB_MA0466.2	8.72504	-	chr4	119454291	119455489	Bcell,Tcell	gene	119454790	119552025	+	start	100	OverlapStart	transcribed_unprocessed_pseudogene	ENSG00000245958	AC093752.1	19.71149
+chr4	121823808	121823818	CEBPB_MA0466.2	8.49634	-	chr4	121822854	121824234	Bcell,Tcell	gene	121816443	121823933	-	start	389	OverlapStart	protein_coding	ENSG00000145386	CCNA2	9.82907
+chr4	123418664	123418674	CEBPB_MA0466.2	8.29482	+	chr4	123418558	123418815	Bcell	gene	123396794	123403760	+	end	14926	Downstream	protein_coding	ENSG00000164056	SPRY1	15.7043
+chr4	127699120	127699130	CEBPB_MA0466.2	8.33809	-	chr4	127698703	127699209	Bcell	gene	127623270	127726737	+	center	23953	PeakInsideFeature	protein_coding	ENSG00000164066	INTU	13.20106
+chr4	128454509	128454519	CEBPB_MA0466.2	8.13744	-	chr4	128454312	128454795	Bcell,Tcell	gene	128292750	128519394	+	center	48481	PeakInsideFeature	lincRNA	ENSG00000251432	AC108062.1	21.81548
+chr4	128812195	128812205	CEBPB_MA0466.2	8.33098	-	chr4	128811187	128812581	Bcell,Tcell	gene	128809622	128875224	+	start	2262	PeakInsideFeature	protein_coding	ENSG00000077684	JADE1	27.73304
+chr4	138406345	138406355	CEBPB_MA0466.2	7.14271	-	chr4	138406243	138406636	Bcell	gene	138309710	138424344	+	end	17905	PeakInsideFeature	lincRNA	ENSG00000251372	LINC00499	15.90565
+chr4	138555750	138555760	CEBPB_MA0466.2	8.51955	-	chr4	138555668	138555899	Bcell	gene	138560703	138561941	+	start	4920	Upstream	processed_pseudogene	ENSG00000248795	AC098859.1	6.21958
+chr4	139454129	139454139	CEBPB_MA0466.2	7.30689	-	chr4	139453041	139454440	Bcell,Tcell	gene	139453231	139476609	+	start	509	OverlapStart	protein_coding	ENSG00000172007	RAB33B	21.68683
+chr4	139528892	139528902	CEBPB_MA0466.2	7.86634	+	chr4	139528739	139528939	Bcell	gene	139495940	139606699	-	center	22480	PeakInsideFeature	protein_coding	ENSG00000145391	SETD7	6.6897
+chr4	140427890	140427900	CEBPB_MA0466.2	10.8789	-	chr4	140426856	140428022	Bcell,Tcell	gene	140388454	140427968	-	start	529	OverlapStart	protein_coding	ENSG00000153132	CLGN	10.78935
+chr4	147943575	147943585	CEBPB_MA0466.2	7.59995	-	chr4	147942765	147943642	Bcell,Tcell	gene	147732062	148072780	+	center	40782	PeakInsideFeature	protein_coding	ENSG00000071205	ARHGAP10	10.2052
+chr4	155072587	155072597	CEBPB_MA0466.2	7.14271	+	chr4	155072252	155072805	Bcell,Tcell	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	6.51077
+chr4	158672245	158672255	CEBPB_MA0466.2	8.52438	-	chr4	158670989	158672747	Bcell,Tcell	gene	158672124	158709623	+	start	256	OverlapStart	protein_coding	ENSG00000171503	ETFDH	35.87337
+chr4	161540233	161540243	CEBPB_MA0466.2	7.64161	-	chr4	161540111	161540651	Bcell	gene	161383896	162164035	-	end	156485	PeakInsideFeature	protein_coding	ENSG00000168843	FSTL5	11.2874
+chr4	163590290	163590300	CEBPB_MA0466.2	7.85922	+	chr4	163590223	163590734	Bcell	gene	163524297	164384050	-	end	66181	PeakInsideFeature	protein_coding	ENSG00000145416	MARCH1	10.8264
+chr4	165613037	165613047	CEBPB_MA0466.2	8.31179	-	chr4	165612990	165613300	Bcell	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	6.07254
+chr4	168790217	168790227	CEBPB_MA0466.2	7.314	-	chr4	168790007	168790306	Bcell	gene	168497065	168928457	+	center	77395	PeakInsideFeature	protein_coding	ENSG00000129116	PALLD	12.72624
+chr4	169294004	169294014	CEBPB_MA0466.2	7.14982	-	chr4	169293305	169294084	Bcell	gene	169094255	169271105	-	start	22589	Downstream	protein_coding	ENSG00000154447	SH3RF1	13.83212
+chr4	170420516	170420526	CEBPB_MA0466.2	8.22916	-	chr4	170420195	170420774	Bcell	gene	170343088	170372311	+	end	48173	Downstream	lincRNA	ENSG00000251061	LINC02512	6.60105
+chr4	170698381	170698391	CEBPB_MA0466.2	7.64161	+	chr4	170697960	170698761	Bcell	gene	170742468	170743718	-	end	44108	Upstream	lincRNA	ENSG00000250968	LINC02382	12.36288
+chr4	172055318	172055328	CEBPB_MA0466.2	8.71296	-	chr4	172055019	172055420	Bcell	gene	171812253	173041559	+	start	242966	PeakInsideFeature	protein_coding	ENSG00000174473	GALNTL6	6.32628
+chr4	174283119	174283129	CEBPB_MA0466.2	7.14982	+	chr4	174283040	174284447	Bcell,Tcell	gene	174283676	174333380	+	start	67	OverlapStart	protein_coding	ENSG00000164118	CEP44	12.94705
+chr4	174358742	174358752	CEBPB_MA0466.2	8.3189	+	chr4	174358389	174359226	Bcell	gene	174354853	174376445	-	end	3954	PeakInsideFeature	lincRNA	ENSG00000249875	AC116616.1	11.46264
+chr4	174882828	174882838	CEBPB_MA0466.2	7.77051	+	chr4	174882439	174882989	Bcell	gene	174829667	174978180	+	center	21209	PeakInsideFeature	protein_coding	ENSG00000168594	ADAM29	7.68334
+chr4	181143420	181143430	CEBPB_MA0466.2	10.8789	+	chr4	181143308	181143566	Bcell,Tcell	gene	181064088	181159149	-	start	15712	PeakInsideFeature	lincRNA	ENSG00000248197	LINC00290	13.51968
+chr4	184314434	184314444	CEBPB_MA0466.2	7.91271	+	chr4	184313983	184314590	Bcell	gene	184299128	184299640	-	start	14646	Downstream	processed_pseudogene	ENSG00000227765	MYL12BP2	17.94634
+chr4	184328683	184328693	CEBPB_MA0466.2	8.25328	-	chr4	184327874	184328763	Bcell,Tcell	gene	184340755	184353977	-	end	12437	Upstream	lincRNA	ENSG00000180712	LINC02363	8.80843
+chr4	184474674	184474684	CEBPB_MA0466.2	7.83515	+	chr4	184473783	184474948	Bcell,Tcell	gene	184387712	184474580	-	start	215	OverlapStart	protein_coding	ENSG00000168310	IRF2	27.74601
+chr4	184537811	184537821	CEBPB_MA0466.2	7.314	-	chr4	184537392	184538342	Bcell,Tcell	gene	184506459	184537554	-	start	313	OverlapStart	lincRNA	ENSG00000271538	LINC02427	9.25092