SCZ 2018 - Brain_Caudate_basal_ganglia
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] 21263#number of imputed weights by chromosome
table(qclist_all$chr)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1943 1490 1296 830 843 1056 1229 736 851 971 1284 1164 399 806 759 863
17 18 19 20 21 22
1510 310 1515 698 42 668 #number of imputed weights without missing variants
sum(qclist_all$nmiss==0)[1] 18726#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)[1] 0.8807INFO: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
0.0095212 0.0003029 gene snp
10.14 10.49 [1] 105318[1] 7589 6309950 gene snp
0.006955 0.190306 [1] 0.01245 1.04773Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
5170 R3HDM2 12_36 0.9660 42.25 3.935e-04 6.634 5 6
2459 FEZF1 7_74 0.9335 24.01 1.987e-04 -4.812 1 1
818 BUB1B-PAK6 15_14 0.8964 29.32 2.257e-04 -5.588 3 3
3475 LINC00320 21_6 0.8236 28.66 2.046e-04 5.336 4 4
1986 DPYSL3 5_86 0.7686 21.57 1.210e-04 -4.157 1 1
1596 CRTAP 3_24 0.7318 21.45 1.099e-04 -3.929 2 2
1866 DHPS 19_10 0.7226 24.07 1.218e-04 -4.396 4 4
740 BDNF 11_19 0.7187 23.36 1.158e-04 4.348 3 3
7165 VPS41 7_28 0.7109 23.67 1.152e-04 -4.509 3 4
2651 GIGYF1 7_62 0.7063 27.02 1.428e-04 -5.266 3 3
5855 SF3B1 2_117 0.6916 44.53 2.064e-04 7.053 3 3
2339 FAM177A1 14_9 0.6862 23.35 1.464e-04 4.820 15 16
4016 MRPS33 7_87 0.6780 23.65 1.081e-04 -4.304 4 5
3407 LAMA5 20_36 0.6684 25.18 1.405e-04 -4.341 14 18
1070 CASP2 7_89 0.6195 20.18 7.356e-05 -3.889 1 1
7343 ZDHHC20 13_2 0.6102 24.33 1.281e-04 -4.784 4 5
2821 GTF2A1 14_39 0.5920 21.85 7.271e-05 4.514 1 1
7077 UQCRC2 16_19 0.5900 22.12 7.312e-05 4.716 1 1
3039 ICE1 5_5 0.5803 24.19 7.734e-05 -3.766 1 1
7349 ZDHHC8 22_4 0.5600 35.56 1.025e-04 -4.861 5 5Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
5170 R3HDM2 12_36 0.9660 42.25 0.0003935 6.634 5 6
818 BUB1B-PAK6 15_14 0.8964 29.32 0.0002257 -5.588 3 3
5855 SF3B1 2_117 0.6916 44.53 0.0002064 7.053 3 3
3475 LINC00320 21_6 0.8236 28.66 0.0002046 5.336 4 4
2459 FEZF1 7_74 0.9335 24.01 0.0001987 -4.812 1 1
2339 FAM177A1 14_9 0.6862 23.35 0.0001464 4.820 15 16
2651 GIGYF1 7_62 0.7063 27.02 0.0001428 -5.266 3 3
3407 LAMA5 20_36 0.6684 25.18 0.0001405 -4.341 14 18
3586 LRP8 1_33 0.5100 31.79 0.0001383 4.820 6 6
454 APOPT1 14_54 0.3793 42.67 0.0001353 7.429 7 9
7343 ZDHHC20 13_2 0.6102 24.33 0.0001281 -4.784 4 5
1859 DGKZ 11_28 0.5285 46.89 0.0001258 7.216 2 2
1866 DHPS 19_10 0.7226 24.07 0.0001218 -4.396 4 4
1986 DPYSL3 5_86 0.7686 21.57 0.0001210 -4.157 1 1
293 AKT3 1_128 0.4197 34.39 0.0001168 -6.291 7 7
740 BDNF 11_19 0.7187 23.36 0.0001158 4.348 3 3
7165 VPS41 7_28 0.7109 23.67 0.0001152 -4.509 3 4
6695 TMEM219 16_24 0.3657 46.18 0.0001112 -7.020 2 2
1596 CRTAP 3_24 0.7318 21.45 0.0001099 -3.929 2 2
4016 MRPS33 7_87 0.6780 23.65 0.0001081 -4.304 4 5Comparing z scores and PIPs
[1] 0.01884 genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
811 BTN2A1 6_20 2.955e-02 107.10 1.303e-06 -11.606 5 5
3622 LSM2 6_26 9.237e-05 214.43 1.737e-11 -11.599 1 1
453 APOM 6_26 1.062e-04 214.01 4.223e-11 11.590 3 3
7130 VARS 6_26 8.850e-05 212.38 1.580e-11 -11.548 1 1
4031 MSH5 6_26 7.912e-05 212.05 2.517e-11 11.538 5 5
690 BAG6 6_26 1.032e-04 208.16 2.116e-11 -11.525 5 7
1742 CYP21A2 6_26 1.973e-05 205.68 7.605e-13 -11.340 1 1
7131 VARS2 6_25 7.654e-02 101.41 5.642e-06 -11.137 1 1
950 C6orf136 6_24 4.467e-02 78.68 2.982e-06 11.031 2 2
2500 FLOT1 6_24 3.719e-02 77.34 5.895e-06 10.981 6 6
814 BTN3A2 6_20 8.558e-02 91.77 7.790e-06 -10.743 6 6
4989 PPT2 6_26 3.156e-05 147.91 1.421e-12 -10.061 5 5
2093 EGFL8 6_26 2.899e-05 147.12 1.191e-12 10.036 6 6
5049 PRRT1 6_26 2.733e-05 146.36 1.038e-12 -10.018 1 1
2773 GPSM3 6_26 2.302e-06 119.97 6.034e-15 9.377 1 1
1157 CCHCR1 6_25 3.504e-02 63.28 8.663e-07 -9.358 11 14
7382 ZKSCAN3 6_22 1.198e-02 54.53 1.404e-07 -9.230 3 3
1805 DDR1 6_25 1.590e-02 67.83 1.627e-07 9.016 1 1
2944 HLA-DMA 6_27 4.411e-02 66.33 1.568e-06 8.781 6 10
4405 NT5C2 10_66 3.004e-01 46.35 8.144e-05 8.475 11 15GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 31Uploading 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 neuron projection development (GO:0010976)
2 peptidyl-L-cysteine S-palmitoylation (GO:0018230)
3 peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine (GO:0018231)
4 modulation of chemical synaptic transmission (GO:0050804)
Overlap Adjusted.P.value Genes
1 3/88 0.04465 BDNF;DPYSL3;LRP8
2 2/23 0.04465 ZDHHC20;ZDHHC8
3 2/23 0.04465 ZDHHC20;ZDHHC8
4 3/109 0.04465 BDNF;LRP8;DGKZ
[1] "GO_Cellular_Component_2021"
Term Overlap Adjusted.P.value
1 U2 snRNP (GO:0005686) 2/20 0.02605
2 U2-type precatalytic spliceosome (GO:0071005) 2/50 0.04407
3 spliceosomal snRNP complex (GO:0097525) 2/51 0.04407
4 precatalytic spliceosome (GO:0071011) 2/52 0.04407
Genes
1 SNRPA1;SF3B1
2 SNRPA1;SF3B1
3 SNRPA1;SF3B1
4 SNRPA1;SF3B1
[1] "GO_Molecular_Function_2021"
Term Overlap
1 protein-cysteine S-palmitoyltransferase activity (GO:0019706) 2/25
2 palmitoyltransferase activity (GO:0016409) 2/29
Adjusted.P.value Genes
1 0.02391 ZDHHC20;ZDHHC8
2 0.02391 ZDHHC20;ZDHHC8DisGeNET enrichment analysis for genes with PIP>0.5
Description
27 Profound Mental Retardation
37 Mental Retardation, Psychosocial
72 Electroencephalogram abnormal
148 Mental deficiency
161 Osteogenesis Imperfecta Type VII
168 MITOCHONDRIAL COMPLEX III DEFICIENCY, NUCLEAR TYPE 5
173 HYPOGONADOTROPIC HYPOGONADISM 22 WITH OR WITHOUT ANOSMIA
177 SPINOCEREBELLAR ATAXIA 42
178 NEURODEVELOPMENTAL DISORDER WITH OR WITHOUT ANOMALIES OF THE BRAIN, EYE, OR HEART
186 SPINOCEREBELLAR ATAXIA 42, EARLY-ONSET, SEVERE, WITH NEURODEVELOPMENTAL DEFICITS
FDR Ratio BgRatio
27 0.05107 3/20 139/9703
37 0.05107 3/20 139/9703
72 0.05107 1/20 1/9703
148 0.05107 3/20 139/9703
161 0.05107 1/20 1/9703
168 0.05107 1/20 1/9703
173 0.05107 1/20 1/9703
177 0.05107 1/20 1/9703
178 0.05107 1/20 1/9703
186 0.05107 1/20 1/9703WebGestalt 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
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
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] 50#significance threshold for TWAS
print(sig_thresh)[1] 4.507#number of ctwas genes
length(ctwas_genes)[1] 4#number of TWAS genes
length(twas_genes)[1] 143#show novel genes (ctwas genes with not in TWAS genes)
ctwas_gene_res[ctwas_gene_res$genename %in% novel_genes,report_cols][1] genename region_tag susie_pip mu2 PVE z num_intron
[8] num_sqtl
<0 rows> (or 0-length row.names)#sensitivity / recall
print(sensitivity) ctwas TWAS
0.01538 0.09231 #specificity
print(specificity) ctwas TWAS
0.9997 0.9826 #precision / PPV
print(precision) ctwas TWAS
0.50000 0.08392
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