Last updated: 2023-08-17

Checks: 2 0

Knit directory: m6A_in_disease_genetics/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

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 06e2427. 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/m6A_switch_to_disease_h2g.nb.html
    Ignored:    data/plots/

Untracked files:
    Untracked:  HMGCR_locus_gene_tracks.pdf
    Untracked:  Rplots.pdf
    Untracked:  analysis/.ipynb_checkpoints/
    Untracked:  analysis/IBD_E_S_m6A.Rmd
    Untracked:  analysis/IBD_E_S_m6A_output.Rmd
    Untracked:  analysis/LDL_E_S_m6A.Rmd
    Untracked:  analysis/LDL_m6A_output.Rmd
    Untracked:  analysis/RA_m6A_output.Rmd
    Untracked:  analysis/WhiteBlood_WholeBlood_E_M.Rmd
    Untracked:  analysis/identify_m6A_mechanisms_with_finemapping.Rmd
    Untracked:  analysis/lymph_m6A_output.Rmd
    Untracked:  analysis/pre_weights_m6AQTL.txt
    Untracked:  analysis/rbc_E_S_m6A_output.Rmd
    Untracked:  analysis/rbc_m6A_output.Rmd
    Untracked:  analysis/wbc_E_S_m6A_output.Rmd
    Untracked:  code/.ipynb_checkpoints/
    Untracked:  code/all_m6a_sites_with_paired_cisNATs_summary.csv
    Untracked:  code/annotating_fine-mapped_m6A_QTLs.Rmd
    Untracked:  code/check_double_strand.ipynb
    Untracked:  code/check_double_strand_v2.ipynb
    Untracked:  code/ctwas/
    Untracked:  code/figure/
    Untracked:  code/learn_gviz.Rmd
    Untracked:  code/learn_gviz.html
    Untracked:  code/learn_gviz.nb.html
    Untracked:  code/m6AQTL_finemapping.Rmd
    Untracked:  code/summary_TWAS_coloc_m6A_2023.Rmd
    Untracked:  code/test_gviz.ipynb
    Untracked:  code/twas_genes_PP4_0.3_immune_traits_trackplots.pdf
    Untracked:  data/.ipynb_checkpoints/
    Untracked:  data/ADCY7_gwas_input.tsv
    Untracked:  data/ADCY7_qtl_input.tsv
    Untracked:  data/Allergy_full_coloc.txt
    Untracked:  data/Asthma_full_coloc.txt
    Untracked:  data/CAD_full_coloc.txt
    Untracked:  data/Eosinophil_count_full_coloc.txt
    Untracked:  data/GSE125377_jointPeakReadCount.txt
    Untracked:  data/HMGCR_ctwas_dat.Rd
    Untracked:  data/IBD_full_coloc.txt
    Untracked:  data/JointPeaks.bed
    Untracked:  data/Li2022_dsRNAs.xlsx
    Untracked:  data/Lupus_full_coloc.txt
    Untracked:  data/RA_full_coloc.txt
    Untracked:  data/TABLE1_hg19.txt
    Untracked:  data/TABLE1_hg19.txt.zip
    Untracked:  data/__MACOSX/
    Untracked:  data/coloc_blood_traits.csv
    Untracked:  data/crohns_disease_full_coloc.txt
    Untracked:  data/edit_sites_and_GE_neg_correlated.txt
    Untracked:  data/edit_sites_and_GE_pos_correlated.txt
    Untracked:  data/features
    Untracked:  data/human_EERs.csv
    Untracked:  data/human_EERs.txt
    Untracked:  data/lymph_full_coloc.txt
    Untracked:  data/m6A_TWAS_results.csv
    Untracked:  data/m6a_TWAS_genes.txt
    Untracked:  data/m6a_joint_calling_peaks.csv
    Untracked:  data/nasser_2021_ABC_IBD_genes.txt
    Untracked:  data/nat_sense_pairs.csv
    Untracked:  data/plt_full_coloc.txt
    Untracked:  data/rbc_full_coloc.txt
    Untracked:  data/rdw_full_coloc.txt
    Untracked:  data/reported_AS_targets_S1.txt
    Untracked:  data/reported_AS_wanowska.txt
    Untracked:  data/sig_coloc_results/
    Untracked:  data/test_locuscomparer.pdf
    Untracked:  data/ulcerative_colitis_full_coloc.txt
    Untracked:  data/wbc_full_coloc.txt
    Untracked:  data/zhao_silver_genes.csv
    Untracked:  output/.ipynb_checkpoints/
    Untracked:  output/HMGCR_gene_track_plot.pdf
    Untracked:  output/HMGCR_locus_plot.pdf
    Untracked:  output/all_m6a_sites_with_cisNATs.csv
    Untracked:  output/all_m6a_sites_with_paired_cisNATs_summary.csv
    Untracked:  output/all_m6a_sites_with_paired_cisNATs_summary_PP40.3.csv
    Untracked:  output/all_m6a_sites_with_paired_cisNATs_summary_PP40.5.csv
    Untracked:  output/all_m6a_sites_with_paired_cis_NATs.csv
    Untracked:  output/fine_mapped_m6AQTLs_TWAS_genes_highPP4.rds
    Untracked:  output/gene_summary.csv
    Untracked:  output/immune_related_m6A_targets.csv
    Untracked:  output/m6aQTL_dsRNAs_PPP2R3C_PRORP.pdf
    Untracked:  output/m6a_peaks_nearby_dsRNAs.csv
    Untracked:  output/m6a_sites_near_all_dsRNAs_twas.csv
    Untracked:  output/m6a_sites_near_dsRNAs_coloc.csv
    Untracked:  output/m6a_sites_near_dsRNAs_twas.csv
    Untracked:  output/m6a_sites_near_dsRNAs_twas_summary.csv
    Untracked:  output/m6a_sites_overlapping_NAT_twas.csv
    Untracked:  output/m6a_sites_overlapping_dsRNAs_coloc.csv
    Untracked:  output/m6a_sites_overlapping_dsRNAs_twas.csv
    Untracked:  output/m6a_sites_overlapping_dsRegions.csv
    Untracked:  output/m6a_sites_overlapping_dsRegions_coloc.csv
    Untracked:  output/negatively_correlated_genes.txt
    Untracked:  output/postively_correlated_genes.txt
    Untracked:  output/rs1806261_RABEP1-NUP88_focused_locusview.pdf
    Untracked:  output/rs1806261_RABEP1-NUP88_locusview.pdf
    Untracked:  output/rs3177647_MAPKAPK5-AS1-MAPKAPK5_locusview.pdf
    Untracked:  output/rs3204541_DDX55-EIF2B1_locusview.pdf
    Untracked:  output/rs7184802_ADCY7-BRD7_locusview.pdf
    Untracked:  output/rs7184802_ADCY7_locuscompare.pdf
    Untracked:  output/twas_genes_PP4_0.3_immune_traits_trackplots.pdf
    Untracked:  output/twas_genes_PP4_0.5_blood_traits_trackplots.pdf
    Untracked:  output/twas_m6a_sites_with_all_cisNATs.RDS
    Untracked:  output/twas_m6a_sites_with_cisNATs_range.RDS
    Untracked:  output/twas_m6a_sites_with_the_nearest_cisNAT.RDS
    Untracked:  twas_genes_PP4_0.3_immune_traits_trackplots.pdf

Unstaged changes:
    Modified:   analysis/lymph_m6A_output_hg19.Rmd
    Modified:   analysis/m6A_switch_to_disease_h2g.Rmd
    Modified:   analysis/wbc_m6A_output.Rmd

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/index.Rmd) and HTML (docs/index.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
Rmd 06e2427 Jing Gu 2023-08-17 added lupus
html f11f68a Jing Gu 2023-08-16 Build site.
Rmd a1e2443 Jing Gu 2023-08-16 added rbc
html 992e835 Jing Gu 2023-08-16 Build site.
Rmd 22983a7 Jing Gu 2023-08-16 wflow_publish("analysis/index.Rmd")
html 3a4bab9 Jing Gu 2023-08-11 Build site.
Rmd c94ee10 Jing Gu 2023-08-11 wflow_publish(c("analysis/wbc_m6A_output_hg19.Rmd", "analysis/index.Rmd",
html 170a310 Jing Gu 2023-08-10 gene-association with ctwas
html 499f070 Jing Gu 2023-06-19 visualize target sites
Rmd b7a7aa3 Jing Gu 2023-05-09 update
html bc330a2 Jing Gu 2023-04-12 update index page
html 98540ac Jing Gu 2023-04-12 update index page
html 86b31ec Jing Gu 2023-04-12 Build site.
Rmd 0e3b2a9 Jing Gu 2023-04-12 publish the initial files
Rmd c558a6b Jing Gu 2023-03-31 Start workflowr project.

Backgrounds

Genetic variants may act through m6A-switch to cause disease

Test the enrichment for dsRNAs formed by m6A-switch with GWAS variants

Genetic variants contribute to trait through PTR mechanisms

m6A informed fine-mapping

Are predicted m6A QTLs enriched for GWAS signals?

Are predicted m6A QTLs enriched for ClinVar variants?