SCZ - Brain Cortex
sheng Qian
2021-2-6
Last updated: 2022-05-19
Checks: 5 2
Knit directory: cTWAS_analysis/
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library(reticulate)
use_python("/scratch/midway2/shengqian/miniconda3/envs/PythonForR/bin/python",required=T)Weight QC
#number of imputed weights
nrow(qclist_all)[1] 23372#number of imputed weights by chromosome
table(qclist_all$chr)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
2106 1670 1401 900 973 1205 1349 834 978 1043 1384 1297 477 810 795 919
17 18 19 20 21 22
1718 307 1661 776 45 724 #number of imputed weights without missing variants
sum(qclist_all$nmiss==0)[1] 20390#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)[1] 0.8724INFO:numexpr.utils:Note: NumExpr detected 56 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.finish
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionCheck convergence of parameters
| Version | Author | Date |
|---|---|---|
| 2749be9 | sq-96 | 2022-05-12 |
gene snp
0.0082338 0.0003052 gene snp
10.48 10.44 [1] 105318[1] 7742 6309950 gene snp
0.00634 0.19088 [1] 0.01226 1.09222Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
5276 R3HDM2 12_36 0.9626 42.83 3.932e-04 -6.634 7 9
6190 SLC8B1 12_68 0.9203 22.26 2.113e-04 -4.047 10 10
838 BUB1B-PAK6 15_14 0.8866 29.77 2.245e-04 5.588 4 4
5228 PTPRF 1_27 0.7922 35.71 2.266e-04 6.680 6 6
6274 SNRPA1 15_50 0.7822 20.88 1.264e-04 -4.098 4 5
6711 THAP8 19_25 0.7522 21.59 1.160e-04 -3.846 1 2
2004 DPYSL3 5_86 0.7392 22.22 1.153e-04 -4.157 1 1
4482 NTRK3 15_41 0.7287 23.89 1.208e-04 4.457 3 3
1728 CUL3 2_132 0.7051 30.35 1.433e-04 5.777 1 1
2356 FAM177A1 14_9 0.7009 23.31 1.327e-04 4.849 13 16
3193 IRF3 19_34 0.6990 39.57 1.868e-04 -6.461 2 2
1042 CAMKK2 12_74 0.6971 35.27 1.555e-04 4.060 8 10
6340 SPECC1 17_16 0.6837 25.24 1.134e-04 -4.822 4 4
5969 SF3B1 2_117 0.6755 45.12 1.990e-04 7.053 3 3
292 AKT3 1_128 0.6495 34.40 1.497e-04 -6.291 5 5
5230 PTPRK 6_85 0.6490 28.20 1.128e-04 -5.059 1 1
352 ANAPC7 12_67 0.5921 39.18 1.510e-04 6.385 6 6
4057 MRPS33 7_87 0.5692 26.29 8.529e-05 -4.304 6 6
456 APOPT1 14_54 0.5393 43.77 1.593e-04 7.429 4 7
7227 UQCRC2 16_19 0.5211 22.85 5.891e-05 4.716 1 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_intron
5276 R3HDM2 12_36 0.9626 42.83 0.0003932 -6.634 7
693 BAG6 6_26 0.2068 637.42 0.0002588 11.590 9
455 APOM 6_26 0.2068 637.42 0.0002588 11.590 2
5228 PTPRF 1_27 0.7922 35.71 0.0002266 6.680 6
838 BUB1B-PAK6 15_14 0.8866 29.77 0.0002245 5.588 4
6190 SLC8B1 12_68 0.9203 22.26 0.0002113 -4.047 10
5969 SF3B1 2_117 0.6755 45.12 0.0001990 7.053 3
3193 IRF3 19_34 0.6990 39.57 0.0001868 -6.461 2
456 APOPT1 14_54 0.5393 43.77 0.0001593 7.429 4
1042 CAMKK2 12_74 0.6971 35.27 0.0001555 4.060 8
352 ANAPC7 12_67 0.5921 39.18 0.0001510 6.385 6
292 AKT3 1_128 0.6495 34.40 0.0001497 -6.291 5
1728 CUL3 2_132 0.7051 30.35 0.0001433 5.777 1
3510 LINC00320 21_6 0.5057 28.55 0.0001432 5.336 5
2356 FAM177A1 14_9 0.7009 23.31 0.0001327 4.849 13
6274 SNRPA1 15_50 0.7822 20.88 0.0001264 -4.098 4
4482 NTRK3 15_41 0.7287 23.89 0.0001208 4.457 3
6711 THAP8 19_25 0.7522 21.59 0.0001160 -3.846 1
2004 DPYSL3 5_86 0.7392 22.22 0.0001153 -4.157 1
6340 SPECC1 17_16 0.6837 25.24 0.0001134 -4.822 4
num_sqtl
5276 9
693 9
455 2
5228 6
838 4
6190 10
5969 3
3193 2
456 7
1042 10
352 6
292 5
1728 1
3510 5
2356 16
6274 5
4482 3
6711 2
2004 1
6340 4Comparing z scores and PIPs
[1] 0.01899 genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
4777 PGBD1 6_22 3.456e-02 158.26 1.118e-06 -13.087 3 5
455 APOM 6_26 2.068e-01 637.42 2.588e-04 11.590 2 2
693 BAG6 6_26 2.068e-01 637.42 2.588e-04 11.590 9 9
7287 VARS 6_26 1.246e-01 638.44 9.411e-05 -11.548 1 1
1821 DDR1 6_25 1.000e-01 101.67 1.052e-05 -11.175 2 2
966 C6orf136 6_24 4.018e-02 79.81 2.447e-06 11.031 2 2
2518 FLOT1 6_24 3.319e-02 78.48 3.961e-06 10.981 5 6
834 BTN3A2 6_20 2.597e-02 91.92 1.454e-06 -10.759 5 5
831 BTN2A1 6_20 3.717e-02 83.45 1.368e-06 10.185 6 7
2975 HLA-B 6_25 2.129e-02 77.13 4.549e-07 10.155 12 31
5078 PPT2 6_26 4.929e-12 474.58 2.190e-25 -10.061 5 5
2105 EGFL8 6_26 3.928e-12 473.96 7.121e-26 10.036 7 8
5142 PRRT1 6_26 3.440e-12 472.86 5.315e-26 -10.018 1 1
5558 RNF5 6_26 7.171e-13 467.32 2.282e-27 -9.714 1 1
2806 GPSM3 6_26 1.139e-13 424.06 1.045e-28 9.377 2 2
1176 CCHCR1 6_25 1.954e-02 62.94 5.542e-07 -9.376 11 15
7545 ZKSCAN3 6_22 1.192e-02 55.91 9.857e-08 9.321 2 3
2977 HLA-DMB 6_27 3.366e-02 68.96 7.526e-07 8.860 2 2
7734 ZSCAN23 6_22 1.033e-02 45.88 4.652e-08 -8.541 1 1
4470 NT5C2 10_66 2.322e-01 47.55 5.883e-05 -8.511 12 16GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 24Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
Term
1 positive regulation of metaphase/anaphase transition of cell cycle (GO:1902101)
2 positive regulation of mitotic metaphase/anaphase transition (GO:0045842)
3 positive regulation of mitotic sister chromatid separation (GO:1901970)
4 regulation of mitotic metaphase/anaphase transition (GO:0030071)
Overlap Adjusted.P.value Genes
1 2/12 0.009283 ANAPC7;CUL3
2 2/12 0.009283 ANAPC7;CUL3
3 2/12 0.009283 ANAPC7;CUL3
4 2/26 0.033933 ANAPC7;CUL3
[1] "GO_Cellular_Component_2021"
Term Overlap
1 U2 snRNP (GO:0005686) 2/20
2 U2-type precatalytic spliceosome (GO:0071005) 2/50
3 spliceosomal snRNP complex (GO:0097525) 2/51
4 precatalytic spliceosome (GO:0071011) 2/52
5 U2-type spliceosomal complex (GO:0005684) 2/89
6 mitochondrial inner membrane (GO:0005743) 3/328
7 organelle inner membrane (GO:0019866) 3/346
8 mitochondrial respiratory chain complex III (GO:0005750) 1/9
9 mitochondrial respiratory chain complex IV (GO:0005751) 1/10
10 ISWI-type complex (GO:0031010) 1/10
11 intrinsic component of mitochondrial membrane (GO:0098573) 1/12
12 cullin-RING ubiquitin ligase complex (GO:0031461) 2/157
13 prespliceosome (GO:0071010) 1/15
14 U2-type prespliceosome (GO:0071004) 1/15
15 mitochondrial membrane (GO:0031966) 3/469
Adjusted.P.value Genes
1 0.009833 SNRPA1;SF3B1
2 0.016759 SNRPA1;SF3B1
3 0.016759 SNRPA1;SF3B1
4 0.016759 SNRPA1;SF3B1
5 0.038539 SNRPA1;SF3B1
6 0.043076 MRPS33;UQCRC2;SLC8B1
7 0.043076 MRPS33;UQCRC2;SLC8B1
8 0.045364 UQCRC2
9 0.045364 UQCRC2
10 0.045364 CECR2
11 0.045573 SLC8B1
12 0.045573 ANAPC7;CUL3
13 0.045573 SF3B1
14 0.045573 SF3B1
15 0.045573 MRPS33;UQCRC2;SLC8B1
[1] "GO_Molecular_Function_2021"
Term
1 transmembrane receptor protein phosphatase activity (GO:0019198)
2 transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)
3 protein tyrosine phosphatase activity (GO:0004725)
4 U2 snRNA binding (GO:0030620)
5 dihydropyrimidinase activity (GO:0004157)
6 calcium:cation antiporter activity (GO:0015368)
7 protein tyrosine kinase activity (GO:0004713)
Overlap Adjusted.P.value Genes
1 2/16 0.00377 PTPRK;PTPRF
2 2/16 0.00377 PTPRK;PTPRF
3 2/74 0.04849 PTPRK;PTPRF
4 1/5 0.04849 SNRPA1
5 1/6 0.04849 DPYSL3
6 1/6 0.04849 SLC8B1
7 2/108 0.04849 NTRK3;CAMKK2DisGeNET enrichment analysis for genes with PIP>0.5
Description
34 Congenital absent nipple
55 Congenital absence of breast with absent nipple
78 PSEUDOHYPOALDOSTERONISM, TYPE IIE
80 MITOCHONDRIAL COMPLEX III DEFICIENCY, NUCLEAR TYPE 5
83 MEGALENCEPHALY-POLYMICROGYRIA-POLYDACTYLY-HYDROCEPHALUS SYNDROME 2
84 BREASTS AND/OR NIPPLES, APLASIA OR HYPOPLASIA OF, 2
85 ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED (HERPES-SPECIFIC), SUSCEPTIBILITY TO, 7
65 Refractory anemia with ringed sideroblasts
68 Congenital Mesoblastic Nephroma
8 Fibrosarcoma
FDR Ratio BgRatio
34 0.01665 1/13 1/9703
55 0.01665 1/13 1/9703
78 0.01665 1/13 1/9703
80 0.01665 1/13 1/9703
83 0.01665 1/13 1/9703
84 0.01665 1/13 1/9703
85 0.01665 1/13 1/9703
65 0.02589 1/13 2/9703
68 0.02589 1/13 2/9703
8 0.02911 1/13 3/9703WebGestalt enrichment analysis for genes with PIP>0.5
Warning: replacing previous import 'lifecycle::last_warnings' by
'rlang::last_warnings' when loading 'hms'Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...Warning in oraEnrichment(interestGeneList, referenceGeneList, geneSet, minNum =
minNum, : No significant gene set is identified based on FDR 0.05!NULLPIP Manhattan Plot
Sensitivity, specificity and precision for silver standard genes
#number of genes in known annotations
print(length(known_annotations))[1] 130#number of genes in known annotations with imputed expression
print(sum(known_annotations %in% ctwas_gene_res$genename))[1] 53#significance threshold for TWAS
print(sig_thresh)[1] 4.511#number of ctwas genes
length(ctwas_genes)[1] 3#number of TWAS genes
length(twas_genes)[1] 147#show novel genes (ctwas genes with not in TWAS genes)
ctwas_gene_res[ctwas_gene_res$genename %in% novel_genes,report_cols] genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
6190 SLC8B1 12_68 0.9203 22.26 0.0002113 -4.047 10 10#sensitivity / recall
print(sensitivity) ctwas TWAS
0.007692 0.107692 #specificity
print(specificity) ctwas TWAS
0.9997 0.9827 #precision / PPV
print(precision) ctwas TWAS
0.33333 0.09524
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
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.4.0 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.3 tidyverse_1.3.1 tibble_3.1.7
[9] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0 cowplot_1.1.1
[13] ggplot2_3.3.5 dplyr_1.0.7 reticulate_1.25 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 doParallel_1.0.16 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 doRNG_1.8.2
[9] bslib_0.2.5.1 utf8_1.2.1 R6_2.5.0 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.2 ggrastr_1.0.1
[17] tidyselect_1.1.1 processx_3.5.2 curl_4.3.2 compiler_4.1.0
[21] git2r_0.28.0 rvest_1.0.0 cli_3.0.0 Cairo_1.5-15
[25] xml2_1.3.2 labeling_0.4.2 sass_0.4.0 scales_1.1.1
[29] callr_3.7.0 systemfonts_1.0.4 apcluster_1.4.9 digest_0.6.27
[33] rmarkdown_2.9 svglite_2.0.0 pkgconfig_2.0.3 htmltools_0.5.1.1
[37] dbplyr_2.1.1 highr_0.9 rlang_1.0.2 rstudioapi_0.13
[41] jquerylib_0.1.4 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[45] magrittr_2.0.1 Matrix_1.3-3 ggbeeswarm_0.6.0 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.0 stringi_1.6.2
[53] whisker_0.4 yaml_2.2.1 plyr_1.8.6 grid_4.1.0
[57] ggrepel_0.9.1 parallel_4.1.0 promises_1.2.0.1 crayon_1.4.1
[61] lattice_0.20-44 haven_2.4.1 hms_1.1.0 knitr_1.33
[65] ps_1.6.0 pillar_1.7.0 igraph_1.2.6 rjson_0.2.20
[69] rngtools_1.5 reshape2_1.4.4 codetools_0.2-18 reprex_2.0.0
[73] glue_1.4.2 evaluate_0.14 getPass_0.2-2 modelr_0.1.8
[77] data.table_1.14.0 png_0.1-7 vctrs_0.3.8 httpuv_1.6.1
[81] foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[85] xfun_0.24 broom_0.7.8 later_1.2.0 iterators_1.0.13
[89] beeswarm_0.4.0 ellipsis_0.3.2 here_1.0.1