SCZ - Brain Cortex
sheng Qian
2021-2-6
Last updated: 2022-10-18
Checks: 5 2
Knit directory: cTWAS_analysis/
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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
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$susie_pip, xlim=c(0,1), main="Distribution of Gene PIPs")
#genes with PIP>0.8 or 20 highest PIPs
head(ctwas_gene_res[order(-ctwas_gene_res$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':
IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'The following object is masked from 'package:base':
expand.gridLoading required package: IRangesLoading required package: GenomicRangesLoading required package: GenomeInfoDbLoading required package: grid
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
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[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] 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
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 rjson_0.2.20
[3] ellipsis_0.3.2 rprojroot_2.0.3
[5] htmlTable_2.2.1 biovizBase_1.42.0
[7] XVector_0.34.0 base64enc_0.1-3
[9] fs_1.5.2 dichromat_2.0-0.1
[11] rstudioapi_0.13 farver_2.1.0
[13] bit64_4.0.5 AnnotationDbi_1.56.1
[15] fansi_1.0.3 xml2_1.3.2
[17] splines_4.1.0 cachem_1.0.6
[19] knitr_1.33 Formula_1.2-4
[21] jsonlite_1.8.0 Rsamtools_2.10.0
[23] cluster_2.1.2 dbplyr_2.1.1
[25] png_0.1-7 compiler_4.1.0
[27] httr_1.4.3 backports_1.2.1
[29] lazyeval_0.2.2 assertthat_0.2.1
[31] Matrix_1.3-3 fastmap_1.1.0
[33] cli_3.3.0 later_1.2.0
[35] htmltools_0.5.3 prettyunits_1.1.1
[37] tools_4.1.0 gtable_0.3.0
[39] glue_1.6.2 GenomeInfoDbData_1.2.7
[41] dplyr_1.0.9 rappdirs_0.3.3
[43] Rcpp_1.0.9 Biobase_2.54.0
[45] jquerylib_0.1.4 vctrs_0.4.1
[47] Biostrings_2.62.0 rtracklayer_1.54.0
[49] xfun_0.24 stringr_1.4.0
[51] ps_1.7.0 lifecycle_1.0.1
[53] ensembldb_2.18.4 restfulr_0.0.13
[55] XML_3.99-0.6 getPass_0.2-2
[57] zlibbioc_1.40.0 scales_1.2.0
[59] BSgenome_1.62.0 VariantAnnotation_1.40.0
[61] ProtGenerics_1.26.0 hms_1.1.1
[63] promises_1.2.0.1 MatrixGenerics_1.6.0
[65] parallel_4.1.0 SummarizedExperiment_1.24.0
[67] AnnotationFilter_1.18.0 RColorBrewer_1.1-3
[69] yaml_2.2.1 curl_4.3.2
[71] gridExtra_2.3 memoise_2.0.1
[73] sass_0.4.0 rpart_4.1-15
[75] biomaRt_2.50.0 latticeExtra_0.6-29
[77] stringi_1.7.6 RSQLite_2.2.14
[79] highr_0.9 BiocIO_1.4.0
[81] checkmate_2.0.0 GenomicFeatures_1.46.1
[83] filelock_1.0.2 BiocParallel_1.28.0
[85] rlang_1.0.4 pkgconfig_2.0.3
[87] matrixStats_0.62.0 bitops_1.0-7
[89] evaluate_0.15 lattice_0.20-44
[91] purrr_0.3.4 htmlwidgets_1.5.3
[93] GenomicAlignments_1.30.0 labeling_0.4.2
[95] bit_4.0.4 processx_3.5.3
[97] tidyselect_1.1.2 magrittr_2.0.3
[99] R6_2.5.1 generics_0.1.2
[101] Hmisc_4.5-0 DelayedArray_0.20.0
[103] DBI_1.1.2 foreign_0.8-81
[105] pillar_1.7.0 whisker_0.4
[107] withr_2.5.0 nnet_7.3-16
[109] survival_3.2-11 KEGGREST_1.34.0
[111] RCurl_1.98-1.6 tibble_3.1.7
[113] crayon_1.5.1 utf8_1.2.2
[115] BiocFileCache_2.2.0 rmarkdown_2.9
[117] jpeg_0.1-8.1 progress_1.2.2
[119] data.table_1.14.2 blob_1.2.3
[121] callr_3.7.0 git2r_0.28.0
[123] digest_0.6.29 httpuv_1.6.1
[125] munsell_0.5.0 bslib_0.4.0