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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/explore_mtsplice.Rmd) and HTML (docs/explore_mtsplice.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
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.)

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."

Version Author Date
a2a8fae Jing Gu 2022-10-01

Version Author Date
a2a8fae Jing Gu 2022-10-01

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

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