Last updated: 2023-11-20
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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head(num_weights,5) tissue number of weights
43 Thyroid 2341
42 Testis 2240
1 Adipose_Subcutaneous 2057
25 Esophagus_Mucosa 2056
30 Lung 2055tail(num_weights,5) tissue number of weights
15 Brain_Hypothalamus 268
14 Brain_Hippocampus 211
8 Brain_Anterior_cingulate_cortex_BA24 208
18 Brain_Spinal_cord_cervical_c-1 194
7 Brain_Amygdala 125results[["Adipose_Subcutaneous"]][["group_pve"]] SNP gene
0.0684186051 0.0003157631 results[["Adipose_Subcutaneous"]][["top_genes"]] id susie_pip
373346 NM_001908|CTSB|chr8|- 0.6739060
737980 NM_014248|RBX1|chr22|+ 0.4111174
741598 NR_037640|HEATR8-TTC4|chr1|+ 0.4084906
529313 NM_018457|PRR13|chr12|+ 0.4004120
271829 NM_022754|SFXN1|chr5|+ 0.3738829results[["Adipose_Visceral_Omentum"]][["group_pve"]] SNP gene
0.0733057330 0.0003479959 results[["Adipose_Visceral_Omentum"]][["top_genes"]] id susie_pip
738212 NM_014248|RBX1|chr22|+ 0.5716242
289590 NM_000287|PEX6|chr6|- 0.5493644
123118 NM_014160|MKRN2|chr3|+ 0.5143896
736925 NM_030882|APOL2|chr22|- 0.5038247
467148 NM_015631|TCTN3|chr10|- 0.4559593results[["Lung"]][["group_pve"]] SNP gene
6.896433e-02 2.152813e-05 results[["Lung"]][["top_genes"]] id susie_pip
302137 NM_001168398|SLC35A1|chr6|+ 0.18840850
81522 NM_000542|SFTPB|chr2|- 0.14079800
737356 NM_030882|APOL2|chr22|- 0.09186556
265111 NM_205836|FBXO38|chr5|+ 0.09130455
700610 NM_005628|SLC1A5|chr19|- 0.06109755results[["Liver"]][["group_pve"]] SNP gene
0.0731320284 0.0003870427 results[["Liver"]][["top_genes"]] id susie_pip
289005 NM_000287|PEX6|chr6|- 0.7966261
373173 NM_001908|CTSB|chr8|- 0.7774279
740747 NM_000379|XDH|chr2|- 0.7661409
352168 NM_015395|TECPR1|chr7|- 0.6405067
286012 NM_000544|TAP2|chr6|- 0.6191271results[["Whole_Blood"]][["group_pve"]] SNP gene
0.0667958155 0.0009569112 results[["Whole_Blood"]][["top_genes"]] id susie_pip
743863 NM_001136033|PUF60|chr8|- 0.9840494
748229 NM_016320|NUP98|chr11|- 0.9747243
766126 NM_014248|RBX1|chr22|+ 0.8872658
741442 NM_006908|RAC1|chr7|+ 0.8722609
289203 NM_000287|PEX6|chr6|- 0.7749128
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
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] cowplot_1.1.1 ggplot2_3.4.0 RSQLite_2.2.19 data.table_1.14.6
[5] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 lattice_0.20-44 getPass_0.2-2 ps_1.7.2
[5] assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.31 foreach_1.5.2
[9] utf8_1.2.2 R6_2.5.1 evaluate_0.19 httr_1.4.4
[13] pillar_1.8.1 rlang_1.1.1 rstudioapi_0.14 whisker_0.4.1
[17] callr_3.7.3 jquerylib_0.1.4 blob_1.2.3 Matrix_1.3-3
[21] rmarkdown_2.19 labeling_0.4.2 stringr_1.5.0 bit_4.0.5
[25] munsell_0.5.0 compiler_4.1.0 httpuv_1.6.7 xfun_0.35
[29] pkgconfig_2.0.3 htmltools_0.5.4 tidyselect_1.2.0 tibble_3.1.8
[33] logging_0.10-108 codetools_0.2-18 ctwas_0.1.40 fansi_1.0.3
[37] dplyr_1.0.10 withr_2.5.0 later_1.3.0 grid_4.1.0
[41] jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3
[45] git2r_0.30.1 magrittr_2.0.3 scales_1.2.1 cli_3.6.1
[49] stringi_1.7.8 cachem_1.0.6 farver_2.1.0 fs_1.5.2
[53] promises_1.2.0.1 pgenlibr_0.3.2 bslib_0.4.1 vctrs_0.6.3
[57] generics_0.1.3 iterators_1.0.14 tools_4.1.0 bit64_4.0.5
[61] glue_1.6.2 processx_3.8.0 fastmap_1.1.0 yaml_2.3.6
[65] colorspace_2.0-3 memoise_2.0.1 knitr_1.41 sass_0.4.4