LDL - Liver
sheng Qian
2022-10-18
Last updated: 2022-10-18
Checks: 5 2
Knit directory: cTWAS_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6a4ec7a | sq-96 | 2022-10-18 | updtae |
| html | 6a4ec7a | sq-96 | 2022-10-18 | updtae |
Weight QC
[1] 12714[1] 10901
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1070 768 652 417 494 611 548 408 405 434 634 629 195 365 354 526
17 18 19 20 21 22
663 160 859 306 114 289 [1] 0.8365Load ctwas results
Check convergence of parameters
| Version | Author | Date |
|---|---|---|
| 6a4ec7a | sq-96 | 2022-10-18 |
gene snp
0.0096829 0.0001743 gene snp
45.772 9.687 [1] 55.56[1] 343621[1] 10901 8696600 gene snp
0.01406 0.04273 [1] 0.05679 gene
0.2476 Genes with highest PIPs
#distribution of PIPs
hist(ctwas_gene_res$susie_pip, xlim=c(0,1), main="Distribution of Gene PIPs")
| Version | Author | Date |
|---|---|---|
| 6a4ec7a | sq-96 | 2022-10-18 |
#genes with PIP>0.8 or 20 highest PIPs
head(ctwas_gene_res[order(-ctwas_gene_res$susie_pip),report_cols], max(sum(ctwas_gene_res$susie_pip>0.8), 20)) genename region_tag susie_pip mu2 PVE z num_eqtl
4435 PSRC1 1_67 1.0000 1675.70 4.877e-03 -41.687 1
12008 HPR 16_38 1.0000 164.01 4.773e-04 -17.963 2
3721 INSIG2 2_69 1.0000 68.69 1.999e-04 -8.983 3
5563 ABCG8 2_27 1.0000 313.97 9.137e-04 -20.294 1
5991 FADS1 11_34 0.9999 164.33 4.782e-04 12.926 2
12687 RP4-781K5.7 1_121 0.9997 203.89 5.932e-04 -15.108 1
10657 TRIM39 6_24 0.9986 72.24 2.099e-04 8.840 3
7410 ABCA1 9_53 0.9954 70.43 2.040e-04 7.982 1
8531 TNKS 8_12 0.9911 76.67 2.211e-04 11.039 2
9390 GAS6 13_62 0.9883 71.42 2.054e-04 -8.924 1
1597 PLTP 20_28 0.9877 61.48 1.767e-04 -5.732 1
1999 PRKD2 19_33 0.9859 30.13 8.645e-05 5.072 2
7040 INHBB 2_70 0.9824 74.11 2.119e-04 -8.519 1
5544 CNIH4 1_114 0.9776 40.86 1.163e-04 6.146 2
2092 SP4 7_19 0.9775 102.48 2.915e-04 10.693 1
6093 CSNK1G3 5_75 0.9749 84.33 2.392e-04 9.116 1
8865 FUT2 19_33 0.9665 105.00 2.953e-04 -11.927 1
11790 CYP2A6 19_28 0.9616 32.05 8.969e-05 5.407 1
3247 KDSR 18_35 0.9547 24.71 6.865e-05 -4.526 1
233 NPC1L1 7_32 0.9526 87.19 2.417e-04 -10.762 1
4704 DDX56 7_32 0.9466 60.02 1.654e-04 9.642 2
6391 TTC39B 9_13 0.9362 23.31 6.349e-05 -4.334 3
6778 PKN3 9_66 0.9360 47.70 1.299e-04 -6.621 1
6220 PELO 5_31 0.9352 70.89 1.929e-04 8.288 2
1114 SRRT 7_62 0.9336 32.81 8.915e-05 5.425 2
3300 C10orf88 10_77 0.9322 37.26 1.011e-04 -6.788 2
8579 STAT5B 17_25 0.9261 30.73 8.281e-05 5.426 2
3562 ACVR1C 2_94 0.9228 25.91 6.960e-05 -4.687 2
6957 USP1 1_39 0.8945 254.14 6.616e-04 16.258 1
9062 KLHDC7A 1_13 0.8163 22.65 5.380e-05 4.124 1
8418 POP7 7_62 0.8091 40.51 9.539e-05 -5.845 1
9072 SPTY2D1 11_13 0.8084 33.57 7.898e-05 -5.557 1Comparing z scores and PIPs
Loading required package: S4VectorsLoading required package: stats4Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'The following objects are masked from 'package:stats':
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Attaching package: 'S4Vectors'The following object is masked from 'package:base':
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sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
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attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Gviz_1.38.4 GenomicRanges_1.46.0 GenomeInfoDb_1.26.7
[4] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.40.0
[7] cowplot_1.1.1 ggplot2_3.3.6 workflowr_1.7.0
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[13] bit64_4.0.5 AnnotationDbi_1.56.1
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[19] knitr_1.33 Formula_1.2-4
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[41] dplyr_1.0.9 rappdirs_0.3.3
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[49] xfun_0.24 stringr_1.4.0
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[69] yaml_2.2.1 curl_4.3.2
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