0610-EA-results

In [11]:

setwd("/storage11_7T/fuy/pig_s/results")
library(readxl)

In [13]:

read_xlsx("0603/2020-06-04diffPeak.LD.Fst_Pi.xlsx")

A tibble: 5 × 5
Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
<chr>	<dbl>	<dbl>	<dbl>	<dbl>
muscle	0.1055	0.06165	0.7751	0.000
small_intestine	0.0113	0.00990	0.1908	0.034
cerebellum	0.0394	0.03790	0.0560	0.042
cerebrum	0.0631	0.06505	-0.0439	0.053
liver	0.0446	0.05585	-0.3245	0.095

In [19]:

read_xlsx("2020-06-09diffPeak.EW.Fst_Pi.xlsx")

A tibble: 5 × 5
Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
<chr>	<dbl>	<dbl>	<dbl>	<dbl>
cerebrum	0.0872	0.06390	0.4485	0.044
small_intestine	0.0133	0.01080	0.3004	0.246
muscle	0.0783	0.06810	0.2014	0.146
cerebellum	0.0419	0.04065	0.0437	0.411
liver	0.0562	0.05820	-0.0504	0.636

In [5]:

readRDS("2020-06-09diffPeak.LD.XPEHH.rds")

A data.frame: 5 × 5
	Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
	<fct>	<dbl>	<dbl>	<dbl>	<dbl>
3	cerebellum	0.0498	0.0408	0.2876	0.005
1	muscle	0.0820	0.0699	0.2303	0.013
12	small_intestine	0.0120	0.0107	0.1654	0.280
11	cerebrum	0.0653	0.0636	0.0381	0.415
2	liver	0.0569	0.0581	-0.0301	0.628

In [6]:

readRDS("2020-06-09diffPeak.EW.XPEHH.rds")

A data.frame: 5 × 5
	Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
	<fct>	<dbl>	<dbl>	<dbl>	<dbl>
3	cerebellum	0.0551	0.0416	0.4055	0.000
11	cerebrum	0.0831	0.0635	0.3881	0.006
1	muscle	0.0902	0.0703	0.3596	0.000
12	small_intestine	0.0114	0.0108	0.0780	0.397
2	liver	0.0574	0.0584	-0.0249	0.627

In [26]:

read_xlsx("2020-06-10diffPeak.LD.XPEHH_Fst_Pi_LD.xlsx")

A tibble: 5 × 5
Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
<chr>	<dbl>	<dbl>	<dbl>	<dbl>
muscle	0.1068	0.0638	0.7433	0.087
cerebellum	0.0533	0.0391	0.4470	0.228
liver	0.0641	0.0554	0.2104	0.339
cerebrum	0.0588	0.0625	-0.0880	0.549
small_intestine	0.0000	0.0086	NA	1.000

In [45]:

read_xlsx("2020-06-10diffPeak.EW.XPEHH_Fst_Pi_EW.xlsx")

A tibble: 5 × 5
Tissues	ratio.real	ratio.sim.mean	log2FC	pVal
<chr>	<dbl>	<dbl>	<dbl>	<dbl>
cerebrum	0.1159	0.06250	0.8910	0.020
small_intestine	0.0184	0.01070	0.7821	0.094
muscle	0.0987	0.06890	0.5185	0.030
cerebellum	0.0539	0.04105	0.3929	0.099
liver	0.0619	0.05805	0.0926	0.370

In [23]:

read_xlsx("2020-06-04.LD.Fst_Pi.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
liver	895	584	0.6159	0.000	6267	6692	-0.0947	1.000	0.7106
heart	1157	867	0.4163	0.000	6005	6409	-0.0939	1.000	0.5102
cerebrum	252	186	0.4381	0.000	6910	7085	-0.0361	0.986	0.4742
muscle	892	774	0.2047	0.000	6270	6500	-0.0520	0.999	0.2567
cerebellum	268	251	0.0945	0.125	6894	7024	-0.0270	0.939	0.1215
lung	849	805	0.0768	0.073	6313	6464	-0.0341	0.974	0.1109
small_intestine	482	469	0.0394	0.256	6680	6804	-0.0265	0.928	0.0659
adipose	448	503	-0.1671	0.995	6714	6777	-0.0135	0.784	-0.1536
pancreas	396	455	-0.2004	0.998	6766	6821	-0.0117	0.754	-0.1887
stomach	103	136	-0.4010	1.000	7059	7132	-0.0148	0.797	-0.3862

In [22]:

read_xlsx("2020-06-09ncd_Fst_Pi_EW.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
cerebellum	721	372	0.9547	0.000	10524	10468	0.0077	0.286	0.9470
stomach	352	204	0.7870	0.000	10893	10640	0.0339	0.005	0.7531
cerebrum	450	276	0.7053	0.000	10795	10563	0.0313	0.015	0.6740
small_intestine	1007	699	0.5267	0.000	10238	10147	0.0129	0.189	0.5138
heart	1794	1294	0.4713	0.000	9451	9548	-0.0147	0.854	0.4860
lung	1571	1199	0.3899	0.000	9674	9640	0.0051	0.377	0.3848
liver	1152	872	0.4017	0.000	10093	9970	0.0177	0.117	0.3840
muscle	1377	1156	0.2524	0.000	9868	9692	0.0260	0.035	0.2264
pancreas	747	680	0.1356	0.005	10498	10163	0.0468	0.001	0.0888
adipose	760	751	0.0172	0.359	10485	10089	0.0555	0.000	-0.0383

In [20]:

read_xlsx("2020-06-09ncd_XPEHH_LD.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
cerebrum	952	779	0.2893	0.000	27782	29709	-0.0967	1	0.3860
cerebellum	1239	1049	0.2402	0.000	27495	29441	-0.0987	1	0.3389
small_intestine	2096	1966	0.0924	0.002	26638	28525	-0.0987	1	0.1911
heart	3771	3640	0.0510	0.017	24963	26851	-0.1052	1	0.1562
liver	2460	2453	0.0041	0.450	26274	28039	-0.0938	1	0.0979
muscle	3163	3240	-0.0347	0.927	25571	27242	-0.0913	1	0.0566
stomach	527	575	-0.1258	0.971	28207	29910	-0.0846	1	-0.0412
lung	3093	3377	-0.1267	1.000	25641	27118	-0.0808	1	-0.0459
pancreas	1694	1912	-0.1746	1.000	27040	28592	-0.0805	1	-0.0941
adipose	1604	2110	-0.3956	1.000	27130	28377	-0.0648	1	-0.3308

In [27]:

read_xlsx("2020-06-10ncd_XPEHH_EW.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
cerebellum	1838	1161	0.6628	0.000	29870	32659	-0.1288	1	0.7916
cerebrum	1224	864	0.5025	0.000	30484	32963	-0.1128	1	0.6153
adipose	2960	2340	0.3391	0.000	28748	31487	-0.1313	1	0.4704
liver	2923	2721	0.1033	0.000	28785	31096	-0.1114	1	0.2147
muscle	3841	3598	0.0943	0.000	27867	30208	-0.1164	1	0.2107
lung	3690	3743	-0.0206	0.820	28018	30084	-0.1026	1	0.0820
stomach	621	637	-0.0367	0.742	31087	33173	-0.0937	1	0.0570
pancreas	2047	2120	-0.0506	0.936	29661	31699	-0.0959	1	0.0453
heart	3781	4032	-0.0927	1.000	27927	29785	-0.0929	1	0.0002
small_intestine	1765	2180	-0.3047	1.000	29943	31631	-0.0791	1	-0.2256

In [46]:

read_xlsx("2020-06-10ncd_XPEHH_Fst_Pi_EW.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
cerebellum	488	136	1.8433	0.000	3711	3849	-0.0527	0.991	1.8960
cerebrum	250	102	1.2934	0.000	3949	3884	0.0239	0.128	1.2695
stomach	133	74	0.8458	0.000	4066	3908	0.0572	0.007	0.7886
small_intestine	416	257	0.6948	0.000	3783	3731	0.0200	0.196	0.6748
liver	486	321	0.5984	0.000	3713	3667	0.0180	0.216	0.5804
heart	698	475	0.5553	0.000	3501	3514	-0.0053	0.586	0.5606
pancreas	318	250	0.3471	0.000	3881	3739	0.0538	0.009	0.2933
muscle	529	424	0.3192	0.000	3670	3564	0.0423	0.041	0.2769
lung	500	441	0.1811	0.000	3699	3546	0.0609	0.006	0.1202
adipose	302	276	0.1299	0.061	3897	3711	0.0706	0.001	0.0593

In [54]:

read_xlsx("2020-06-11ncd_XPEHH_Fst_Pi_LD.xlsx")

A tibble: 10 × 10
tissues	DEG_real	DEG_sim	DEG_log2FC	DEG_pVal	nonDEG_real	nonDEG_sim	nonDEG_log2FC	nonDEG_pVal	delta_log2FC
<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
cerebellum	118	45	1.3908	0.000	1242	1271	-0.0333	0.805	1.4241
cerebrum	89	34	1.3883	0.000	1271	1281	-0.0113	0.624	1.3996
stomach	44	24	0.8745	0.000	1316	1291	0.0277	0.246	0.8468
liver	177	106	0.7397	0.000	1183	1210	-0.0326	0.775	0.7723
small_intestine	142	85	0.7404	0.000	1218	1231	-0.0153	0.651	0.7557
heart	232	157	0.5634	0.000	1128	1156	-0.0354	0.802	0.5988
muscle	170	140	0.2801	0.004	1190	1174	0.0195	0.316	0.2606
pancreas	83	83	0.0000	0.502	1277	1235	0.0482	0.122	-0.0482
lung	110	146	-0.4085	1.000	1250	1169	0.0967	0.008	-0.5052
adipose	3	90	-4.9069	1.000	1357	1224	0.1488	0.000	-5.0557

In [53]:

a = read_xlsx("table/Fst_Pi_EW_ATAC_DEG_daf09.xlsx")
head(a)
dim(a)

A tibble: 6 × 5
GeneID	lc	D	DE	tissue
<chr>	<dbl>	<dbl>	<dbl>	<chr>
BCL2L15	0	1	-3.038876	muscle
DCLRE1B	0	1	-1.476660	muscle
LRRC14B	1	0	1.314285	muscle
NPC2	0	2	-1.397972	muscle
NT5C2	0	1	-1.073619	muscle
PCGF6	0	1	-1.390373	muscle

In [49]:

dim(read_xlsx("table/XPEHH_LD_ATAC_DEG_daf09.xlsx"))

In [50]:

dim(read_xlsx("table/XPEHH_EW_ATAC_DEG_daf09.xlsx"))

In [51]:

dim(read_xlsx("table/XPEHH_Fst_Pi_LD_ATAC_DEG_daf09.xlsx"))

In [52]:

dim(read_xlsx("table/XPEHH_Fst_Pi_EW_ATAC_DEG_daf09.xlsx"))