explore_mtsplice
2022-09-20
Last updated: 2022-10-07
Checks: 6 1
Knit directory: funcFinemapping/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 9e4e697 | Jing Gu | 2022-10-07 | understand mtsplice outputs |
| html | a2a8fae | Jing Gu | 2022-10-01 | explore MTSplice |
MMSplice/MTSplice predictions
MTSplice model \[ \Delta logit(\Psi_{e,t}) = logit(\Psi_{e,avg}^{ref} ) + \text{MMSplice}(S_{ref}-S_{alt}) + \text{TSplice}(S_{alt}, \text{tissue}) - logit(\Psi_{e,t}^{ref}) \] MMSplice model \[ \Delta logit(\Psi_{e,t}) = logit(\Psi_{e,avg}^{ref} ) + \text{MMSplice}(S_{ref}-S_{alt}) - logit(\Psi_{e,t}^{ref}) \]
Understand MTSplice outputs.
Three types of outputs
Tissue_ref: psi scores for ref allele in one tissue
Tissue_delta_psi: difference in psi scores between ref and alt
Tissue:logit psi difference between ref and alt
Version Author Date a2a8fae Jing Gu 2022-10-01
Distribution of the location of predicted SNPs
Warning in sprintf("%s%% predicted SNPs are within 5kb from the nearest exon", :
one argument not used by format '%s%% predicted SNPs are within 5kb from the
nearest exon'
| Version | Author | Date |
|---|---|---|
| a2a8fae | Jing Gu | 2022-10-01 |
Majority of MTSplice predicted SNPs are within 500 bp from the nearest exon.
MMSplice predictions on ASD de novo mutations
Replicate the results in fig 7a using the reported de novo mutations from ASD patients (Zhou et al.) The de novo mutations were filtered by 1) within exons or their 300-nt flanking intronic regions and 2) having MMSplice predicted \(\Delta\text{logit}(\Psi)\) with a magnitude greater than 0.05.
Legend:
- The color specifies whether an individual is a proband or sibling.
- The dot on the plot represents mean predicted scores and error bar stands for 95% confidence interval
[1] "The number of mutations that satisfy the criteria is 3725, very close to 3884 mutations found in the paper."
Compare with Spidex results
data directory: /home/jinggu/cluster/data/features/raw/splicing/spidex
Around 3000 out of 3700 de novo variants with splicing
altering effects were found in Spidex predictions.
| Version | Author | Date |
|---|---|---|
| a2a8fae | Jing Gu | 2022-10-01 |
In our analysis, MMSplice or Spidex now shows comparable results as the ones displayed on Fig 7a from the paper. The main difference is confidence interval was drawn instead of standard deviation.
sessionInfo()R version 4.2.0 (2022-04-22)
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 LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.3.6 dplyr_1.0.9 data.table_1.14.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.2 xfun_0.30 bslib_0.3.1 reshape2_1.4.4
[5] purrr_0.3.4 colorspace_2.0-3 vctrs_0.4.1 generics_0.1.2
[9] htmltools_0.5.2 yaml_2.3.5 utf8_1.2.2 rlang_1.0.2
[13] R.oo_1.24.0 jquerylib_0.1.4 later_1.3.0 pillar_1.7.0
[17] glue_1.6.2 withr_2.5.0 DBI_1.1.2 R.utils_2.11.0
[21] plyr_1.8.7 lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0
[25] gtable_0.3.0 workflowr_1.7.0 R.methodsS3_1.8.1 evaluate_0.15
[29] labeling_0.4.2 knitr_1.39 fastmap_1.1.0 httpuv_1.6.5
[33] fansi_1.0.3 highr_0.9 Rcpp_1.0.8.3 promises_1.2.0.1
[37] scales_1.2.0 jsonlite_1.8.0 farver_2.1.0 fs_1.5.2
[41] digest_0.6.29 stringi_1.7.6 rprojroot_2.0.3 grid_4.2.0
[45] cli_3.3.0 tools_4.2.0 magrittr_2.0.3 sass_0.4.1
[49] tibble_3.1.7 crayon_1.5.1 whisker_0.4 pkgconfig_2.0.3
[53] ellipsis_0.3.2 assertthat_0.2.1 rmarkdown_2.14 rstudioapi_0.13
[57] R6_2.5.1 git2r_0.30.1 compiler_4.2.0