CI calculation added for odds ratio

analyses/interaction-plots/results/cooccur_top50.Embryonal-tumor.tsv

@@ -1,37 +1,37 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-CTNNB1	DDX3X	5	7	4	118	21.071428571428573	1	2.4802290387181266e-4	0.004464412269692628	3.6055082120534396	12	9	8.955223880597014	6.7164179104477615	31.25	68.75
-CTNNB1	KMT2D	2	10	6	116	3.8666666666666667	1	0.1521221251649965	0.608488500659986	0.8178076160701827	12	8	8.955223880597014	5.970149253731344	11.11111111111111	88.88888888888889
-CTNNB1	TTN	0	12	7	115	0	-1	1	1	0	12	7	8.955223880597014	5.223880597014926	0	100
-CTNNB1	TP53	5	7	2	120	42.857142857142854	1	4.540242466151527e-5	0.0016344872878145498	4.34292095355262	12	7	8.955223880597014	5.223880597014926	35.714285714285715	64.28571428571429
-CTNNB1	KMT2C	0	12	7	115	0	-1	1	1	0	12	7	8.955223880597014	5.223880597014926	0	100
-CTNNB1	KDM6A	0	12	6	116	0	-1	1	1	0	12	6	8.955223880597014	4.477611940298507	0	100
-CTNNB1	PTCH1	0	12	5	117	0	-1	1	1	0	12	5	8.955223880597014	3.7313432835820897	0	100
-CTNNB1	SMARCA4	3	9	2	120	20	1	0.005047038855497565	0.060564466265970784	2.2969633517626034	12	5	8.955223880597014	3.7313432835820897	21.428571428571427	78.57142857142857
-DDX3X	KMT2D	2	7	6	119	5.666666666666667	1	0.0911014729934339	0.4099566284704525	1.0404746009880497	9	8	6.7164179104477615	5.970149253731344	13.333333333333334	86.66666666666667
-DDX3X	TTN	2	7	5	120	6.857142857142857	1	0.07084119623043927	0.36432615204225915	1.1497141138866418	9	7	6.7164179104477615	5.223880597014926	14.285714285714286	85.71428571428571
-DDX3X	TP53	2	7	5	120	6.857142857142857	1	0.07084119623043927	0.36432615204225915	1.1497141138866418	9	7	6.7164179104477615	5.223880597014926	14.285714285714286	85.71428571428571
-DDX3X	KMT2C	1	8	6	119	2.4791666666666665	1	0.39247308984297946	0.7849461796859589	0.40619011556421364	9	7	6.7164179104477615	5.223880597014926	6.666666666666667	93.33333333333333
-DDX3X	KDM6A	0	9	6	119	0	-1	1	1	0	9	6	6.7164179104477615	4.477611940298507	0	100
-DDX3X	PTCH1	2	7	3	122	11.619047619047619	1	0.03626038814899659	0.26107479467277545	1.440567551314279	9	5	6.7164179104477615	3.7313432835820897	16.666666666666668	83.33333333333333
-DDX3X	SMARCA4	2	7	3	122	11.619047619047619	1	0.03626038814899659	0.26107479467277545	1.440567551314279	9	5	6.7164179104477615	3.7313432835820897	16.666666666666668	83.33333333333333
-KMT2D	TTN	1	7	6	120	2.857142857142857	1	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
-KMT2D	TP53	1	7	6	120	2.857142857142857	1	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
-KMT2D	KMT2C	1	7	6	120	2.857142857142857	1	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
-KMT2D	KDM6A	0	8	6	120	0	-1	1	1	0	8	6	5.970149253731344	4.477611940298507	0	100
-KMT2D	PTCH1	0	8	5	121	0	-1	1	1	0	8	5	5.970149253731344	3.7313432835820897	0	100
-KMT2D	SMARCA4	1	7	4	122	4.357142857142857	1	0.2684868006432142	0.7554413917586529	0.5710770602389986	8	5	5.970149253731344	3.7313432835820897	8.333333333333334	91.66666666666667
-TTN	TP53	0	7	7	120	0	-1	0.9999999999999999	1	-4.8216373327664354e-17	7	7	5.223880597014926	5.223880597014926	0	100
-TTN	KMT2C	1	6	6	121	3.361111111111111	1	0.31921249185345635	0.7554413917586529	0.495920121591761	7	7	5.223880597014926	5.223880597014926	7.6923076923076925	92.3076923076923
-TTN	KDM6A	1	6	5	122	4.066666666666666	1	0.2798280905557226	0.7554413917586529	0.5531086909843053	7	6	5.223880597014926	4.477611940298507	8.333333333333334	91.66666666666667
-TTN	PTCH1	1	6	4	123	5.125	1	0.2385067514892475	0.7554413917586529	0.6224993227327814	7	5	5.223880597014926	3.7313432835820897	9.090909090909092	90.9090909090909
-TTN	SMARCA4	0	7	5	122	0	-1	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
-TP53	KMT2C	0	7	7	120	0	-1	0.9999999999999999	1	-4.8216373327664354e-17	7	7	5.223880597014926	5.223880597014926	0	100
-TP53	KDM6A	0	7	6	121	0	-1	0.9999999999999999	1	-4.8216373327664354e-17	7	6	5.223880597014926	4.477611940298507	0	100
-TP53	PTCH1	1	6	4	123	5.125	1	0.2385067514892475	0.7554413917586529	0.6224993227327814	7	5	5.223880597014926	3.7313432835820897	9.090909090909092	90.9090909090909
-TP53	SMARCA4	0	7	5	122	0	-1	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
-KMT2C	KDM6A	0	7	6	121	0	-1	0.9999999999999999	1	-4.8216373327664354e-17	7	6	5.223880597014926	4.477611940298507	0	100
-KMT2C	PTCH1	0	7	5	122	0	-1	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
-KMT2C	SMARCA4	0	7	5	122	0	-1	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
-KDM6A	PTCH1	0	6	5	123	0	-1	1	1	0	6	5	4.477611940298507	3.7313432835820897	0	100
-KDM6A	SMARCA4	0	6	5	123	0	-1	1	1	0	6	5	4.477611940298507	3.7313432835820897	0	100
-PTCH1	SMARCA4	0	5	5	124	0	-1	1	1	0	5	5	3.7313432835820897	3.7313432835820897	0	100
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+CTNNB1	DDX3X	5	7	4	118	21.071428571428573	1	4.95247334385552-89.6532038060717	2.4802290387181266e-4	0.004464412269692628	3.6055082120534396	12	9	8.955223880597014	6.7164179104477615	31.25	68.75
+CTNNB1	KMT2D	2	10	6	116	3.8666666666666667	1	0.788909968938627-18.9516062665881	0.1521221251649965	0.608488500659986	0.8178076160701827	12	8	8.955223880597014	5.970149253731344	11.11111111111111	88.88888888888889
+CTNNB1	TTN	0	12	7	115	0	-1	0-0	1	1	0	12	7	8.955223880597014	5.223880597014926	0	100
+CTNNB1	TP53	5	7	2	120	42.857142857142854	1	8.09120023034498-227.003984772138	4.540242466151527e-5	0.0016344872878145498	4.34292095355262	12	7	8.955223880597014	5.223880597014926	35.714285714285715	64.28571428571429
+CTNNB1	KMT2C	0	12	7	115	0	-1	0-0	1	1	0	12	7	8.955223880597014	5.223880597014926	0	100
+CTNNB1	KDM6A	0	12	6	116	0	-1	0-0	1	1	0	12	6	8.955223880597014	4.477611940298507	0	100
+CTNNB1	PTCH1	0	12	5	117	0	-1	0-0	1	1	0	12	5	8.955223880597014	3.7313432835820897	0	100
+CTNNB1	SMARCA4	3	9	2	120	20	1	3.46754970734058-115.355231722627	0.005047038855497565	0.060564466265970784	2.2969633517626034	12	5	8.955223880597014	3.7313432835820897	21.428571428571427	78.57142857142857
+DDX3X	KMT2D	2	7	6	119	5.666666666666667	1	1.10513867241768-29.0561826425479	0.0911014729934339	0.4099566284704525	1.0404746009880497	9	8	6.7164179104477615	5.970149253731344	13.333333333333334	86.66666666666667
+DDX3X	TTN	2	7	5	120	6.857142857142857	1	1.2945920368552-36.3206375635421	0.07084119623043927	0.36432615204225915	1.1497141138866418	9	7	6.7164179104477615	5.223880597014926	14.285714285714286	85.71428571428571
+DDX3X	TP53	2	7	5	120	6.857142857142857	1	1.2945920368552-36.3206375635421	0.07084119623043927	0.36432615204225915	1.1497141138866418	9	7	6.7164179104477615	5.223880597014926	14.285714285714286	85.71428571428571
+DDX3X	KMT2C	1	8	6	119	2.4791666666666665	1	0.36826402391718-16.6898392510189	0.39247308984297946	0.7849461796859589	0.40619011556421364	9	7	6.7164179104477615	5.223880597014926	6.666666666666667	93.33333333333333
+DDX3X	KDM6A	0	9	6	119	0	-1	0-0	1	1	0	9	6	6.7164179104477615	4.477611940298507	0	100
+DDX3X	PTCH1	2	7	3	122	11.619047619047619	1	1.95424426577384-69.0815728300157	0.03626038814899659	0.26107479467277545	1.440567551314279	9	5	6.7164179104477615	3.7313432835820897	16.666666666666668	83.33333333333333
+DDX3X	SMARCA4	2	7	3	122	11.619047619047619	1	1.95424426577384-69.0815728300157	0.03626038814899659	0.26107479467277545	1.440567551314279	9	5	6.7164179104477615	3.7313432835820897	16.666666666666668	83.33333333333333
+KMT2D	TTN	1	7	6	120	2.857142857142857	1	0.417812716842596-19.5380968004328	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
+KMT2D	TP53	1	7	6	120	2.857142857142857	1	0.417812716842596-19.5380968004328	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
+KMT2D	KMT2C	1	7	6	120	2.857142857142857	1	0.417812716842596-19.5380968004328	0.3567362127749194	0.7554413917586529	0.44765280260428697	8	7	5.970149253731344	5.223880597014926	7.142857142857143	92.85714285714286
+KMT2D	KDM6A	0	8	6	120	0	-1	0-0	1	1	0	8	6	5.970149253731344	4.477611940298507	0	100
+KMT2D	PTCH1	0	8	5	121	0	-1	0-0	1	1	0	8	5	5.970149253731344	3.7313432835820897	0	100
+KMT2D	SMARCA4	1	7	4	122	4.357142857142857	1	0.595866629548654-31.8606428621975	0.2684868006432142	0.7554413917586529	0.5710770602389986	8	5	5.970149253731344	3.7313432835820897	8.333333333333334	91.66666666666667
+TTN	TP53	0	7	7	120	0	-1	0-0	0.9999999999999999	1	-4.8216373327664354e-17	7	7	5.223880597014926	5.223880597014926	0	100
+TTN	KMT2C	1	6	6	121	3.361111111111111	1	0.481624212393378-23.4561876469936	0.31921249185345635	0.7554413917586529	0.495920121591761	7	7	5.223880597014926	5.223880597014926	7.6923076923076925	92.3076923076923
+TTN	KDM6A	1	6	5	122	4.066666666666666	1	0.566978509491917-29.1682621138457	0.2798280905557226	0.7554413917586529	0.5531086909843053	7	6	5.223880597014926	4.477611940298507	8.333333333333334	91.66666666666667
+TTN	PTCH1	1	6	4	123	5.125	1	0.687242835435448-38.2188415007014	0.2385067514892475	0.7554413917586529	0.6224993227327814	7	5	5.223880597014926	3.7313432835820897	9.090909090909092	90.9090909090909
+TTN	SMARCA4	0	7	5	122	0	-1	0-0	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
+TP53	KMT2C	0	7	7	120	0	-1	0-0	0.9999999999999999	1	-4.8216373327664354e-17	7	7	5.223880597014926	5.223880597014926	0	100
+TP53	KDM6A	0	7	6	121	0	-1	0-0	0.9999999999999999	1	-4.8216373327664354e-17	7	6	5.223880597014926	4.477611940298507	0	100
+TP53	PTCH1	1	6	4	123	5.125	1	0.687242835435448-38.2188415007014	0.2385067514892475	0.7554413917586529	0.6224993227327814	7	5	5.223880597014926	3.7313432835820897	9.090909090909092	90.9090909090909
+TP53	SMARCA4	0	7	5	122	0	-1	0-0	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
+KMT2C	KDM6A	0	7	6	121	0	-1	0-0	0.9999999999999999	1	-4.8216373327664354e-17	7	6	5.223880597014926	4.477611940298507	0	100
+KMT2C	PTCH1	0	7	5	122	0	-1	0-0	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
+KMT2C	SMARCA4	0	7	5	122	0	-1	0-0	1	1	0	7	5	5.223880597014926	3.7313432835820897	0	100
+KDM6A	PTCH1	0	6	5	123	0	-1	0-0	1	1	0	6	5	4.477611940298507	3.7313432835820897	0	100
+KDM6A	SMARCA4	0	6	5	123	0	-1	0-0	1	1	0	6	5	4.477611940298507	3.7313432835820897	0	100
+PTCH1	SMARCA4	0	5	5	124	0	-1	0-0	1	1	0	5	5	3.7313432835820897	3.7313432835820897	0	100

analyses/interaction-plots/results/cooccur_top50.Ependymal-tumor.tsv

@@ -1,2 +1,2 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-NF2	SLC35A1	0	3	2	60	0	-1	1	1	0	3	2	4.615384615384615	3.076923076923077	0	100
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+NF2	SLC35A1	0	3	2	60	0	-1	0-0	1	1	0	3	2	4.615384615384615	3.076923076923077	0	100

analyses/interaction-plots/results/cooccur_top50.LGAT.tsv

@@ -1,16 +1,16 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-BRAF	FGFR1	0	42	7	163	0	-1	0.3493843776177437	1	-0.4566965179738428	42	7	19.81132075471698	3.30188679245283	0	100
-BRAF	BCOR	0	42	5	165	0	-1	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
-BRAF	IDH1	0	42	5	165	0	-1	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
-BRAF	NF1	1	41	4	166	1.0121951219512195	1	1	1	-0	42	5	19.81132075471698	2.358490566037736	2.1739130434782608	97.82608695652173
-BRAF	PIK3CA	0	42	5	165	0	-1	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
-FGFR1	BCOR	0	7	5	200	0	-1	1	1	0	7	5	3.30188679245283	2.358490566037736	0	100
-FGFR1	IDH1	0	7	5	200	0	-1	1	1	0	7	5	3.30188679245283	2.358490566037736	0	100
-FGFR1	NF1	2	5	3	202	26.933333333333334	1	0.008948537449269297	0.06711403086951973	2.048247940060156	7	5	3.30188679245283	2.358490566037736	20	80
-FGFR1	PIK3CA	3	4	2	203	76.125	1	2.1717282703177644e-4	0.0032575924054766467	3.6631945152176697	7	5	3.30188679245283	2.358490566037736	33.333333333333336	66.66666666666667
-BCOR	IDH1	0	5	5	202	0	-1	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
-BCOR	NF1	0	5	5	202	0	-1	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
-BCOR	PIK3CA	1	4	4	203	12.6875	1	0.11351702328225664	0.5675851164112832	0.9449390057556558	5	5	2.358490566037736	2.358490566037736	11.11111111111111	88.88888888888889
-IDH1	NF1	0	5	5	202	0	-1	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
-IDH1	PIK3CA	0	5	5	202	0	-1	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
-NF1	PIK3CA	0	5	5	202	0	-1	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+BRAF	FGFR1	0	42	7	163	0	-1	0-0	0.3493843776177437	1	-0.4566965179738428	42	7	19.81132075471698	3.30188679245283	0	100
+BRAF	BCOR	0	42	5	165	0	-1	0-0	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
+BRAF	IDH1	0	42	5	165	0	-1	0-0	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
+BRAF	NF1	1	41	4	166	1.0121951219512195	1	0.154615531659309-6.62636511291365	1	1	-0	42	5	19.81132075471698	2.358490566037736	2.1739130434782608	97.82608695652173
+BRAF	PIK3CA	0	42	5	165	0	-1	0-0	0.5854914991868638	1	-0.23247940611345894	42	5	19.81132075471698	2.358490566037736	0	100
+FGFR1	BCOR	0	7	5	200	0	-1	0-0	1	1	0	7	5	3.30188679245283	2.358490566037736	0	100
+FGFR1	IDH1	0	7	5	200	0	-1	0-0	1	1	0	7	5	3.30188679245283	2.358490566037736	0	100
+FGFR1	NF1	2	5	3	202	26.933333333333334	1	4.31718811367226-168.027064224312	0.008948537449269297	0.06711403086951973	2.048247940060156	7	5	3.30188679245283	2.358490566037736	20	80
+FGFR1	PIK3CA	3	4	2	203	76.125	1	11.7016492627854-495.230671750673	2.1717282703177644e-4	0.0032575924054766467	3.6631945152176697	7	5	3.30188679245283	2.358490566037736	33.333333333333336	66.66666666666667
+BCOR	IDH1	0	5	5	202	0	-1	0-0	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
+BCOR	NF1	0	5	5	202	0	-1	0-0	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
+BCOR	PIK3CA	1	4	4	203	12.6875	1	1.60004586521453-100.605026236805	0.11351702328225664	0.5675851164112832	0.9449390057556558	5	5	2.358490566037736	2.358490566037736	11.11111111111111	88.88888888888889
+IDH1	NF1	0	5	5	202	0	-1	0-0	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
+IDH1	PIK3CA	0	5	5	202	0	-1	0-0	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100
+NF1	PIK3CA	0	5	5	202	0	-1	0-0	1	1	0	5	5	2.358490566037736	2.358490566037736	0	100

analyses/interaction-plots/results/cooccur_top50.Meningioma.tsv

@@ -1,2 +1,2 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-NF2	MYH4	2	5	0	12	Inf	1	0.1228070175438596	0.1228070175438596	0.9107768156582348	7	2	36.8421052631579	10.526315789473685	28.571428571428573	71.42857142857143
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+NF2	MYH4	2	5	0	12	Inf	1	Inf-Inf	0.1228070175438596	0.1228070175438596	0.9107768156582348	7	2	36.8421052631579	10.526315789473685	28.571428571428573	71.42857142857143

analyses/interaction-plots/results/cooccur_top50.Neuronal-mixed-neuronal-glial-tumor.tsv

@@ -1,2 +1,2 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-FGFR1	PDGFRA	0	4	2	20	0	-1	1.0000000000000002	1.0000000000000002	9.64327466553287e-17	4	2	15.384615384615385	7.6923076923076925	0	100
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+FGFR1	PDGFRA	0	4	2	20	0	-1	0-0	1.0000000000000002	1.0000000000000002	9.64327466553287e-17	4	2	15.384615384615385	7.6923076923076925	0	100

analyses/interaction-plots/results/cooccur_top50.Tumors-of-sellar-region.tsv

@@ -1,2 +1,2 @@
-gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
-CTNNB1	PHLPP1	1	21	1	5	0.23809523809523808	-1	0.3888888888888889	0.3888888888888889	-0.4101744650890492	22	2	78.57142857142857	7.142857142857143	4.3478260869565215	95.65217391304348
+gene1	gene2	mut11	mut10	mut01	mut00	odds_ratio	cooccur_sign	ci	p	q	cooccur_score	n_mutated_gene1	n_mutated_gene2	perc_mutated_gene1	perc_mutated_gene2	perc_cooccur	perc_mutexcl
+CTNNB1	PHLPP1	1	21	1	5	0.23809523809523808	-1	0.012606678597958-4.49677065716662	0.3888888888888889	0.3888888888888889	-0.4101744650890492	22	2	78.57142857142857	7.142857142857143	4.3478260869565215	95.65217391304348

analyses/interaction-plots/scripts/cooccur_functions.R

@@ -19,6 +19,23 @@ row_fisher <- function(w, x, y, z) {
   return(fisher$p.value)
 }
 
+#' Calculate confidence interval for odds ratio
+#' 
+#' @return CI of odds ratio 
+calc_ci <- function(mut11, mut10, mut01, mut00, odds_ratio){
+  if(sum(mut11==0 | mut10==0 | mut01==0 | mut00==0)>0){
+    standard_error_or <- sqrt(1/(mut11+0.5) + 1/(mut10+0.5) + 1/(mut01+0.5) + 1/(mut00+0.5))
+  } 
+  else {
+    standard_error_or <- sqrt(1/mut11 + 1/mut10 + 1/mut01 + 1/mut00)
+  }
+  or_ci_lower_bound <- exp(log(odds_ratio) - 1.96 * standard_error_or)
+  or_ci_upper_bound <- exp(log(odds_ratio) + 1.96 * standard_error_or)
+
+  ci <- paste0(or_ci_lower_bound, "-", or_ci_upper_bound )
+  return(ci)
+}
+
 #' Filter mutations based on VAF and effect
 #'
 #' @param maf_df a data frame of a maf file or subset of one. Minimally includes
@@ -96,8 +113,9 @@ filter_mutations <- function(maf_df,
 #'  `gene1`; `gene2` (gene names);
 #'  `mut11`; `mut10`; `mut01` (counts of mutations in each category of sharing:
 #'     `mut11`: both mutated; `mut10`: mutated in the first but not second gene, etc.);
-#'  `odds_ratio` (odds ratio for for co-occurence);
+#'  `odds_ratio` (odds ratio for co-occurence);
 #'  `cooccur_sign` (1 if co-occurence greater than by chance, -1 if less frequent than expected)
+#'  `ci` (confidence interval for odds_ratio);
 #'  `p` (the fisher's exact test p value);
 #'  `q` (Benjamini-Hochberg adjusted p value);
 #'  `cooccur_score` (calculated as `cooccur_sign * -log10(p)`);
@@ -152,6 +170,7 @@ coocurrence <- function(gene_sample_df,
       odds_ratio = (mut11 * mut00) / (mut10 * mut01),
       cooccur_sign = ifelse(odds_ratio > 1, 1, -1)
       ) %>%
+    dplyr::mutate(ci=calc_ci(mut11, mut10, mut01, mut00, odds_ratio)) %>% 
     dplyr::rowwise() %>%
     dplyr::mutate(p = row_fisher(mut11, mut10, mut01, mut00)) %>%
     dplyr::ungroup() %>%