Last updated: 2022-10-03
Checks: 1 1
Knit directory: funcFinemapping/
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.
The R Markdown file has unstaged changes. 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.
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 868016b. 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: .RData
Ignored: .ipynb_checkpoints/
Ignored: analysis/.Rhistory
Ignored: analysis/PTR_m6A.nb.html
Ignored: analysis/build_annotations_for_single_cell_data.nb.html
Ignored: analysis/lab4_prepare.nb.html
Ignored: analysis/ldsc_results.nb.html
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
Untracked files:
Untracked: SCZ_pval_vs_MAF.png
Untracked: SNPs_categories,png
Untracked: SNPs_categories.png
Untracked: analysis/.ipynb_checkpoints/
Untracked: analysis/PTR_m6A.Rmd
Untracked: analysis/PTR_splicing_mtsplice.Rmd
Untracked: analysis/PTR_splicing_spliceAI.Rmd
Untracked: analysis/explore_mtsplice.Rmd
Untracked: analysis/snp_finemapping_spliceAI_prior.Rmd
Untracked: analysis/snp_finemapping_with_priors.Rmd
Untracked: bmi_locus1410.pdf
Untracked: code/.ipynb_checkpoints/
Untracked: code/.snakemake/
Untracked: code/Euro_LD_Chunks.RData
Untracked: code/Snakefile
Untracked: code/config.yaml
Untracked: code/environment.yml
Untracked: code/extract_mmsplice_predictions_bychr.R
Untracked: code/extract_mtsplice_maxPred.sh
Untracked: code/get_indiv_annotation_from_predictions.R
Untracked: code/heatmap_torus_enrichment.ipynb
Untracked: code/ldsc.log
Untracked: code/ldsc.results
Untracked: code/ldsc_regression.sh
Untracked: code/make_joint_annotations.R
Untracked: code/make_plots.R
Untracked: code/out/
Untracked: code/plot_torus_enrichment.R
Untracked: code/prepare_torus_inputs.R
Untracked: code/run_ldsc.sh
Untracked: code/run_ldsc_with_bed.sh
Untracked: code/run_ldsc_with_bed_v2.sh
Untracked: code/run_susie.R
Untracked: code/run_susie_in_parallel.R
Untracked: code/run_torus.sh
Untracked: code/run_torus/
Untracked: code/sctype/
Untracked: code/slurm-22619162.out
Untracked: code/slurm-22619163.out
Untracked: code/slurm-22619164.out
Untracked: code/slurm-22619165.out
Untracked: code/slurm-22619166.out
Untracked: code/slurm-22619199.out
Untracked: code/slurm-22619200.out
Untracked: code/slurm-22619201.out
Untracked: code/slurm-22619202.out
Untracked: code/slurm-22619203.out
Untracked: code/slurm-22619228.out
Untracked: code/slurm-22619229.out
Untracked: code/slurm-22619230.out
Untracked: code/slurm-22619231.out
Untracked: code/slurm-22619232.out
Untracked: code/slurm-22619234.out
Untracked: code/slurm-22619235.out
Untracked: code/slurm-22619236.out
Untracked: code/slurm-22619237.out
Untracked: code/slurm-22619238.out
Untracked: code/slurm-22619289.out
Untracked: code/slurm-22619290.out
Untracked: code/split_vcf.sh
Untracked: code/test_mtsplice.txt.gz
Untracked: code_backup/
Untracked: data/ASD_denovo_variants.1.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.10.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.11.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.12.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.13.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.14.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.15.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.16.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.17.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.18.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.19.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.2.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.20.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.21.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.22.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.3.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.4.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.5.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.6.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.7.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.8.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.9.sorted.vcf.gz
Untracked: data/ASD_denovo_variants.vcf.gz
Untracked: data/ScTypeDB_full.xlsx
Untracked: data/compare_spliceai_and_mmsplice.RData
Untracked: data/header.txt.gz
Untracked: data/hg19_gtf_genomic_annots_ver2.gr.rds
Untracked: data/mmsplice_mtsplice_cutoffs.M5.txt
Untracked: data/mmsplice_mtsplice_cutoffs.txt
Untracked: data/num_overlaps_finemapped_SNPs_and_ctcf.txt
Untracked: data/process_vcf.sh
Untracked: data/qqplot_SNPs_high_spliceAI.png
Untracked: data/qqplot_SNPs_high_spliceAI_scores_SCZ.png
Untracked: data/qqplot_SNPs_high_spliceAI_scores_aFib.png
Untracked: data/qqplot_SNPs_high_spliceAI_scores_allergy.png
Untracked: data/spliceAIandMAF.txt.gz
Untracked: data/torus_enrichment_novel_annot.est
Untracked: data/torus_joint_enrichment.est
Untracked: data/torus_joint_refined_enrichment.est
Untracked: data/vcf/
Untracked: enhancer_gene_feature.rmd
Untracked: fig1_panels.pdf
Untracked: fig2.pdf
Untracked: fig_panel2.pdf
Untracked: gene_mapping.pdf
Untracked: output/AAD/GMP_merge_stats.txt
Untracked: output/AAD/Wang2020_joint.results
Untracked: output/AAD/Wang2020_joint_T.results
Untracked: output/AAD/Wang2020_joint_tissueResT.results
Untracked: output/AAD/allergy/Ulirsch2019/GMP_merge_compare_old.est
Untracked: output/AAD/allergy/Ulirsch2019_disjoint_snps.sumstats
Untracked: output/AAD/allergy/Wang2020_T_subsets.est
Untracked: output/AAD/allergy/Wang2020_T_subsets_indiv.est
Untracked: output/AAD/allergy/Wang2020_T_tissueRes.est
Untracked: output/AAD/allergy/Wang2020_joint_T.results
Untracked: output/AAD/allergy/Wang2020_joint_tissueResT.results
Untracked: output/AAD/allergy/Wang2020_tissueResT.est
Untracked: output/AAD/allergy/torus_enrichment_CD4.est
Untracked: output/AAD/allergy/torus_enrichment_CD8.est
Untracked: output/AAD/allergy/torus_enrichment_non_tissueRes_T.est
Untracked: output/AAD/allergy/torus_enrichment_tissueMigraT.est
Untracked: output/AAD/allergy/torus_enrichment_tissueResT_C6.est
Untracked: output/AAD/allergy/torus_enrichment_tissueResT_C8.est
Untracked: output/AAD/allergy/torus_enrichment_tissueRes_T.est
Untracked: output/AAD/allergy/torus_enrichment_tissueResident_T_cells.est
Untracked: output/AAD/asthma_adult/Ulirsch2019/CD4_compare_old.est
Untracked: output/AAD/asthma_adult/Ulirsch2019/CD8_compare_old.est
Untracked: output/AAD/asthma_adult/Ulirsch2019/GMP_merge_compare_old.est
Untracked: output/AAD/asthma_adult/Wang2020_T_subsets.est
Untracked: output/AAD/asthma_adult/Wang2020_T_subsets_indiv.est
Untracked: output/AAD/asthma_adult/Wang2020_T_tissueRes.est
Untracked: output/AAD/asthma_adult/Wang2020_joint_T.results
Untracked: output/AAD/asthma_adult/Wang2020_joint_tissueResT.results
Untracked: output/AAD/asthma_adult/torus_enrichment_CD4.est
Untracked: output/AAD/asthma_adult/torus_enrichment_CD8.est
Untracked: output/AAD/asthma_adult/torus_enrichment_non_tissueRes_T.est
Untracked: output/AAD/asthma_adult/torus_enrichment_tissueMigraT.est
Untracked: output/AAD/asthma_adult/torus_enrichment_tissueResT_C6.est
Untracked: output/AAD/asthma_adult/torus_enrichment_tissueResT_C8.est
Untracked: output/AAD/asthma_adult/torus_enrichment_tissueRes_T.est
Untracked: output/AAD/asthma_adult/torus_enrichment_tissueResident_T_cells.est
Untracked: output/AAD/asthma_child/CD4_compare.est
Untracked: output/AAD/asthma_child/CD8_compare.est
Untracked: output/AAD/asthma_child/Ulirsch2019/GMP_merge_compare_old.est
Untracked: output/AAD/asthma_child/Ulirsch2019/torus_enrichment_CD4.est
Untracked: output/AAD/asthma_child/Ulirsch2019/torus_enrichment_CD8.est
Untracked: output/AAD/asthma_child/Wang2020_T_subsets.est
Untracked: output/AAD/asthma_child/Wang2020_T_subsets_indiv.est
Untracked: output/AAD/asthma_child/Wang2020_T_tissueRes.est
Untracked: output/AAD/asthma_child/Wang2020_joint_T.results
Untracked: output/AAD/asthma_child/Wang2020_joint_tissueResT.results
Untracked: output/AAD/asthma_child/torus_enrichment_CD4.est
Untracked: output/AAD/asthma_child/torus_enrichment_CD8.est
Untracked: output/AAD/asthma_child/torus_enrichment_non_tissueRes_T.est
Untracked: output/AAD/asthma_child/torus_enrichment_tissueMigraT.est
Untracked: output/AAD/asthma_child/torus_enrichment_tissueResT_C6.est
Untracked: output/AAD/asthma_child/torus_enrichment_tissueResT_C8.est
Untracked: output/AAD/asthma_child/torus_enrichment_tissueRes_T.est
Untracked: output/AAD/asthma_child/torus_enrichment_tissueResident_T_cells.est
Untracked: output/LDL_ukb_L10.gif
Untracked: output/LDL_ukb_L10.pdf
Untracked: output/background_SNPs_annotated_percent.txt
Untracked: output/ldsc
Untracked: output/locus_1452.gif
Untracked: output/locus_1452.pdf
Untracked: output/spliceAI_vs_MAF.png
Untracked: output/splicing/.ipynb_checkpoints/
Untracked: output/splicing/PTR_across_traits_annotations.results
Untracked: output/splicing/PTR_joint.pdf
Untracked: output/splicing/PTR_joint.png
Untracked: output/splicing/QQplot_mmsplice.png
Untracked: output/splicing/QQplot_mmsplice_top15.png
Untracked: output/splicing/QQplot_mmsplice_vs_mtsplice.png
Untracked: output/splicing/QQplot_mmsplice_vs_mtsplice_SCZ.png
Untracked: output/splicing/TSplice_scores_distribution.png
Untracked: output/splicing/aFib_joint_comparison.pdf
Untracked: output/splicing/allergy_joint_comparison.pdf
Untracked: output/splicing/header.txt
Untracked: output/splicing/m6A_enrichment_across_traits.pdf
Untracked: output/splicing/mmsplice_vs_mtsplice_AA_heart.png
Untracked: output/splicing/mmsplice_vs_mtsplice_Hypothalamus_brain.png
Untracked: output/splicing/mmsplice_vs_mtsplice_LV_heart.png
Untracked: output/splicing/mmsplice_vs_mtsplice_across_tissues.png
Untracked: output/splicing/mtsplice_enrichment_across_traits.pdf
Untracked: output/splicing/prior/
Untracked: output/splicing/scz_PTR_annotations.results
Untracked: output/splicing/scz_joint_comparison.pdf
Untracked: output/splicing/scz_neuOCR_m6a_DMR.results
Untracked: output/splicing/scz_spliceAI0.03_hist.png
Untracked: output/splicing/scz_spliceAI0.03_scatterplot.png
Untracked: output/splicing/scz_spliceai_binary0.03.results
Untracked: output/splicing/summarizing_aFib_PIPs.pdf
Untracked: output/splicing/torus_afib_spliceai.est
Untracked: output/splicing/torus_annotations_spliceai0.01.txt.gz
Untracked: output/splicing/torus_annotations_spliceai0.03.txt.gz
Untracked: output/splicing/torus_annotations_spliceai0.05.txt.gz
Untracked: output/splicing/torus_annotations_spliceai0.07.txt.gz
Untracked: output/splicing/torus_annotations_spliceai0.1.txt.gz
Untracked: output/splicing/torus_annotations_spliceai0.2.txt.gz
Untracked: output/splicing/torus_annotations_spliceai9.txt.gz
Untracked: output/splicing/torus_enrichment_joint_scz_mtsplice0.6_hypothalamus-brain.est
Untracked: output/splicing/torus_enrichment_joint_scz_spliceAI.est
Untracked: output/splicing/torus_spliceai0.01.enrichment
Untracked: output/splicing/torus_spliceai0.03.enrichment
Untracked: output/splicing/torus_spliceai0.05.enrichment
Untracked: output/splicing/torus_spliceai0.07.enrichment
Untracked: output/splicing/torus_spliceai0.1.enrichment
Untracked: output/splicing/torus_spliceai0.2.enrichment
Untracked: output/splicing/torus_zscores.txt.gz
Untracked: output/torus
Untracked: panel_figure2.pdf
Untracked: test.txt
Unstaged changes:
Deleted: .Rprofile
Modified: analysis/index.Rmd
Modified: analysis/lab4_prepare.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
Deleted: output/AAD/asthma/Caldero2019_diffDA_annot_percent.txt
Deleted: output/AAD/asthma/Caldero2019_stimuDA_annot_percent.txt
Deleted: output/AAD/asthma/celltype_specific_adult_lungs_torus.est
Deleted: output/AAD/asthma/diffe_adult_blood_torus.est
Deleted: output/AAD/asthma/joint_blood_immune_rest_vs_stimu.est
Deleted: output/AAD/asthma/joint_lung_vs_blood_immune_diff_torus.est
Deleted: output/AAD/asthma/joint_lung_vs_blood_immune_stimu_torus.est
Deleted: output/AAD/asthma/lung_clusters_dict.txt
Deleted: output/AAD/asthma/lung_clusters_info.txt
Deleted: output/AAD/asthma/stimu_adult_blood_torus.est
Deleted: output/AAD/asthma/torus_enrichment_all_rest.est
Deleted: output/AAD/asthma/torus_enrichment_all_stimulated.est
Deleted: output/AAD/asthma/zhang2021_annot_percent.txt
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.
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 |
|---|---|---|---|---|
| html | a2a8fae | Jing Gu | 2022-10-01 | explore MTSplice |
| html | b3909a4 | Jing Gu | 2022-08-17 | fine-mapping with spliceAI priors |
| html | 8e55d5a | Jing Gu | 2022-08-02 | update index |
| html | 0fbd86a | Jing Gu | 2022-07-02 | update index |
| html | d96f416 | Jing Gu | 2022-06-15 | estimate_h2g |
| html | ccdd167 | Jing Gu | 2022-06-15 | estimate_h2g |
| html | 8c82e64 | Jing Gu | 2022-06-15 | Build site. |
| Rmd | 611b343 | Jing Gu | 2022-06-15 | wflow_publish(files = c("analysis/index.Rmd", "docs/ldsc_PTR_results.html")) |
| html | 27f0ead | Jing Gu | 2022-06-04 | wflow_publish(files = c("docs/index.html", "docs/exploring_lung_scATAC_R.html", |
| html | a71a34d | Jing Gu | 2022-03-24 | Build site. |
| Rmd | 5ea9a98 | Jing Gu | 2022-03-24 | update spliceAI results |
| html | 506928d | Jing Gu | 2022-03-23 | analyzed snATAC-seq lung dataset |
| html | 5b65bd1 | Jing Gu | 2021-10-26 | Build site. |
| Rmd | db3c6f9 | Jing Gu | 2021-10-26 | test enrichment for asthma risk variants |
| html | 53a8774 | Jing Gu | 2021-09-22 | Build site. |
| html | 2a6fc91 | Jing Gu | 2021-09-22 | Build site. |
| html | 41f53c8 | Jing Gu | 2021-09-22 | Build site. |
| html | b0b938b | Jing Gu | 2021-09-22 | Build site. |
| Rmd | 8a5656c | Jing Gu | 2021-09-22 | analyzed Asthma GWAS with functional priors from single cell data |
| html | 639aacf | Jing Gu | 2021-09-08 | Build site. |
| html | c046e9e | Jing Gu | 2021-09-08 | Build site. |
| html | 05f73e9 | Jing Gu | 2021-09-01 | Build site. |
| Rmd | bed838e | Jing Gu | 2021-09-01 | update evaluations on slicing |
| html | bbfe1d4 | Jing Gu | 2021-04-22 | Build site. |
| html | 540e287 | Jing Gu | 2021-04-21 | Build site. |
| html | e597d4e | Jing Gu | 2021-04-21 | Build site. |
| html | 491ca5c | Jing Gu | 2021-04-14 | Build site. |
| html | ba251cb | Jing Gu | 2021-04-14 | Build site. |
| html | 66c75b9 | Jing Gu | 2021-04-06 | Build site. |
| html | 1a76b29 | Jing Gu | 2021-04-06 | Build site. |
| Rmd | ae12e8a | Jing Gu | 2021-04-06 | evaluate sequence constraints |
| html | 752cb39 | Jing Gu | 2021-04-05 | Build site. |
| html | f1c5950 | Jing Gu | 2021-04-05 | Build site. |
| Rmd | 5e70ecc | Jing Gu | 2021-04-05 | edit index page |
| html | d16a5e0 | Jing Gu | 2021-04-05 | Build site. |
| Rmd | 6f7214b | Jing Gu | 2021-04-05 | edit index page |
| html | 4d851a8 | Jing Gu | 2021-04-05 | Build site. |
| Rmd | 4cc091d | Jing Gu | 2021-04-05 | start my phd project |
| html | 12fa9ff | Jing Gu | 2021-04-04 | Build site. |
| Rmd | c00a877 | Jing Gu | 2021-04-04 | Start workflowr project. |
My thesis project is about improving functional fine mapping procedures that enable us to identify causal variants underlying complex traits such as obsesity and asthma.
This document will provide an overview of my thesis project, including the aims for the project, summary of previous work, details of the method, and preliminary results. By constantly reviewing this document, I can keep track of my research aims without getting diverted too far.