PTR:RNA-modifications

workflowr

• Summary
• Checks
• Past versions

Last updated: 2022-08-02

Checks: 6 1

Knit directory: funcFinemapping/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: uncommitted changes

The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you'll want to first commit it to the Git repo. If you're still working on the analysis, you can ignore this warning. When you're finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it's best to always run the code in an empty environment.

Seed: set.seed(20210404)

The command set.seed(20210404) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: abda215

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version abda215. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .ipynb_checkpoints/
    Ignored:    analysis/PTR_m6A.nb.html
    Ignored:    analysis/build_annotations_for_single_cell_data.nb.html
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    Ignored:    analysis/learn_archR.nb.html
    Ignored:    analysis/mtsplice_finemapping_results.nb.html
    Ignored:    analysis/results.nb.html
    Ignored:    analysis/snp_finemapping_results.nb.html
    Ignored:    analysis/splicing.nb.html
    Ignored:    analysis/susie_tutorial.nb.html

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Unstaged changes:
    Deleted:    .Rprofile
    Modified:   analysis/index.Rmd
    Modified:   analysis/ldsc_PTR_results.Rmd
    Deleted:    output/AAD/Caldero2019_disjoint_snps.sumstats
    Modified:   output/AAD/allergy/Caldero2019_disjoint_snps.sumstats
    Modified:   output/AAD/allergy/Ulirsch2019/GMP_merge_compare.est
    Modified:   output/AAD/allergy/Wang2020_indiv.est
    Modified:   output/AAD/allergy/Wang2020_joint.results
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    Deleted:    output/AAD/asthma/zhang2021_cell_type_overlaps.txt
    Deleted:    output/AAD/asthma/zhang2021_peaks_per_celltype.txt
    Modified:   output/AAD/asthma_adult/Ulirsch2019/CD4_compare.est
    Modified:   output/AAD/asthma_adult/Ulirsch2019/CD8_compare.est
    Deleted:    output/AAD/asthma_adult/Ulirsch2019/GMP_merge_compare.est
    Modified:   output/AAD/asthma_adult/Wang2020_indiv.est
    Modified:   output/AAD/asthma_adult/Wang2020_joint.results
    Modified:   output/AAD/asthma_child/Ulirsch2019/GMP_merge_compare.est
    Modified:   output/AAD/asthma_child/Wang2020_indiv.est
    Modified:   output/AAD/asthma_child/Wang2020_joint.results
    Deleted:    output/asthma/Caldero2019_diffDA_annot_percent.txt
    Deleted:    output/asthma/Caldero2019_stimuDA_annot_percent.txt
    Deleted:    output/asthma/celltype_specific_adult_lungs_torus.est
    Deleted:    output/asthma/diffe_adult_blood_torus.est
    Deleted:    output/asthma/joint_lung_vs_blood_immune_diff_torus.est
    Deleted:    output/asthma/joint_lung_vs_blood_immune_stimu_torus.est
    Deleted:    output/asthma/lung_clusters_dict.txt
    Deleted:    output/asthma/lung_clusters_info.txt
    Deleted:    output/asthma/stimu_adult_blood_torus.est
    Deleted:    output/asthma/zhang2021_annot_percent.txt
    Deleted:    output/asthma/zhang2021_cell_type_overlaps.txt
    Deleted:    output/asthma/zhang2021_peaks_per_celltype.txt

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.

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Backgrounds

Post-transcriptional regulatory (PTR) processes have been implicated in development and diseases, however, it is largely unknown how genetic variations are mediated through PTR processes. We propose to annotate GWAS variants using both experimental measurements and computational predictions. With this prior knowledge, we can further identify most likely causal variants through fine-mapping and then link them to genes.

Several post-transcriptonal features will be explored:

• alternative splicing
• RNA modification: m6A
• RNA binding
• Polyadenylation

Results

LDSC enrichment across multiple traits

Session information

sessionInfo()

R version 4.0.4 (2021-02-15)
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] ggplot2_3.3.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8        highr_0.8         pillar_1.5.0      compiler_4.0.4   
 [5] bslib_0.2.4       later_1.1.0.1     jquerylib_0.1.3   git2r_0.28.0     
 [9] workflowr_1.6.2   tools_4.0.4       digest_0.6.27     jsonlite_1.7.2   
[13] evaluate_0.14     lifecycle_1.0.0   tibble_3.0.6      gtable_0.3.0     
[17] pkgconfig_2.0.3   rlang_1.0.1       DBI_1.1.1         cli_3.2.0        
[21] rstudioapi_0.13   yaml_2.2.1        xfun_0.21         withr_2.4.3      
[25] dplyr_1.0.4       stringr_1.4.0     knitr_1.31        generics_0.1.0   
[29] fs_1.5.0          vctrs_0.3.8       sass_0.3.1        tidyselect_1.1.1 
[33] rprojroot_2.0.2   grid_4.0.4        glue_1.6.1        R6_2.5.1         
[37] fansi_1.0.2       rmarkdown_2.7     farver_2.1.0      purrr_0.3.4      
[41] magrittr_2.0.1    scales_1.1.1      promises_1.2.0.1  ellipsis_0.3.2   
[45] htmltools_0.5.1.1 assertthat_0.2.1  colorspace_2.0-2  httpuv_1.5.5     
[49] labeling_0.4.2    utf8_1.2.2        stringi_1.5.3     munsell_0.5.0    
[53] crayon_1.4.1