Last updated: 2022-03-01

Checks: 1 1

Knit directory: cTWAS_analysis/

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 601071b. 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:    data/AF/

Untracked files:
    Untracked:  Rplot.png
    Untracked:  analysis/.ipynb_checkpoints/
    Untracked:  analysis/Autism_Brain_Amygdala.Rmd
    Untracked:  analysis/Autism_Brain_Anterior_cingulate_cortex_BA24.Rmd
    Untracked:  analysis/Autism_Brain_Caudate_basal_ganglia.Rmd
    Untracked:  analysis/Autism_Brain_Cerebellar_Hemisphere.Rmd
    Untracked:  analysis/Autism_Brain_Cerebellum.Rmd
    Untracked:  analysis/Autism_Brain_Cortex.Rmd
    Untracked:  analysis/Autism_Brain_Frontal_Cortex_BA9.Rmd
    Untracked:  analysis/Autism_Brain_Hippocampus.Rmd
    Untracked:  analysis/Autism_Brain_Hypothalamus.Rmd
    Untracked:  analysis/Autism_Brain_Nucleus_accumbens_basal_ganglia.Rmd
    Untracked:  analysis/Autism_Brain_Putamen_basal_ganglia.Rmd
    Untracked:  analysis/Autism_Brain_Spinal_cord_cervical_c-1.Rmd
    Untracked:  analysis/Autism_Brain_Substantia_nigra.Rmd
    Untracked:  analysis/BMI_results.Rmd
    Untracked:  analysis/Glucose_Adipose_Subcutaneous.Rmd
    Untracked:  analysis/Glucose_Adipose_Visceral_Omentum.Rmd
    Untracked:  analysis/Splicing_Test.Rmd
    Untracked:  code/.ipynb_checkpoints/
    Untracked:  code/AF_out/
    Untracked:  code/Autism_out/
    Untracked:  code/BMI_S_out/
    Untracked:  code/BMI_out/
    Untracked:  code/Glucose_out/
    Untracked:  code/LDL_S_out/
    Untracked:  code/SCZ_S_out/
    Untracked:  code/SCZ_out/
    Untracked:  code/T2D_out/
    Untracked:  code/ctwas_config.R
    Untracked:  code/mapping.R
    Untracked:  code/out/
    Untracked:  code/run_AF_analysis.sbatch
    Untracked:  code/run_AF_analysis.sh
    Untracked:  code/run_AF_ctwas_rss_LDR.R
    Untracked:  code/run_Autism_analysis.sbatch
    Untracked:  code/run_Autism_analysis.sh
    Untracked:  code/run_Autism_ctwas_rss_LDR.R
    Untracked:  code/run_BMI_analysis.sbatch
    Untracked:  code/run_BMI_analysis.sh
    Untracked:  code/run_BMI_analysis_S.sbatch
    Untracked:  code/run_BMI_analysis_S.sh
    Untracked:  code/run_BMI_ctwas_rss_LDR.R
    Untracked:  code/run_BMI_ctwas_rss_LDR_S.R
    Untracked:  code/run_Glucose_analysis.sbatch
    Untracked:  code/run_Glucose_analysis.sh
    Untracked:  code/run_Glucose_ctwas_rss_LDR.R
    Untracked:  code/run_LDL_analysis_S.sbatch
    Untracked:  code/run_LDL_analysis_S.sh
    Untracked:  code/run_LDL_ctwas_rss_LDR_S.R
    Untracked:  code/run_SCZ_analysis.sbatch
    Untracked:  code/run_SCZ_analysis.sh
    Untracked:  code/run_SCZ_analysis_S.sbatch
    Untracked:  code/run_SCZ_analysis_S.sh
    Untracked:  code/run_SCZ_ctwas_rss_LDR.R
    Untracked:  code/run_SCZ_ctwas_rss_LDR_S.R
    Untracked:  code/run_T2D_analysis.sbatch
    Untracked:  code/run_T2D_analysis.sh
    Untracked:  code/run_T2D_ctwas_rss_LDR.R
    Untracked:  data/.ipynb_checkpoints/
    Untracked:  data/Autism/
    Untracked:  data/BMI/
    Untracked:  data/BMI_S/
    Untracked:  data/Glucose/
    Untracked:  data/LDL_S/
    Untracked:  data/SCZ/
    Untracked:  data/SCZ_S/
    Untracked:  data/T2D/
    Untracked:  data/TEST/
    Untracked:  data/UKBB/
    Untracked:  data/UKBB_SNPs_Info.text
    Untracked:  data/gene_OMIM.txt
    Untracked:  data/gene_pip_0.8.txt
    Untracked:  data/mashr_Heart_Atrial_Appendage.db
    Untracked:  data/mashr_sqtl/
    Untracked:  data/summary_known_genes_annotations.xlsx
    Untracked:  data/untitled.txt

Unstaged changes:
    Modified:   analysis/index.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
html 3829e82 sq-96 2022-03-01 wq
html b2cb1a0 sq-96 2022-02-28 Build site.
Rmd 83b0e36 sq-96 2022-02-28 update
html 26c9b3f sq-96 2022-02-28 Build site.
Rmd 5da5f1f sq-96 2022-02-28 update
html 48ac0f3 sq-96 2022-02-27 Build site.
Rmd 25c7a37 sq-96 2022-02-27 update
html 0593225 sq-96 2022-02-23 Build site.
Rmd 5135a74 sq-96 2022-02-23 update
html f7ec8c2 sq-96 2022-02-22 Build site.
Rmd 6d4c4c9 sq-96 2022-02-22 update
html 753dc32 sq-96 2022-02-22 Build site.
Rmd 4b58620 sq-96 2022-02-22 update
html bb3a946 sq-96 2022-02-14 Build site.
Rmd 0ade7d3 sq-96 2022-02-14 update
html d20e424 sq-96 2022-02-14 Build site.
Rmd 67211e8 sq-96 2022-02-14 update
html 91f38fa sq-96 2022-02-13 Build site.
html e6bc169 sq-96 2022-02-13 Build site.
Rmd 87fee8b sq-96 2022-02-13 update
html 4106919 sq-96 2021-12-24 Build site.
html 1f785cf sq-96 2021-12-22 Build site.
html 82c68fd sq-96 2021-12-22 Build site.
html 9cf0e70 sq-96 2021-12-22 Build site.
html 77de9fb sq-96 2021-12-22 Build site.
html 6b46de7 sq-96 2021-12-22 Build site.
html e22d0c9 sq-96 2021-12-21 Build site.
Rmd a6c7890 sq-96 2021-12-21 Start my new project
html a8dbae0 sq-96 2021-12-21 Build site.
html 564d909 sq-96 2021-12-20 Build site.
html e080e7b sq-96 2021-12-20 Build site.
html 9b1bb6e sq-96 2021-12-20 Build site.
html 773dcb5 sq-96 2021-12-20 Build site.
html d6eccf8 sq-96 2021-12-20 Build site.
Rmd 2d5ef03 sq-96 2021-12-20 Publish the files
html 3052d49 sq-96 2021-12-20 Build site.
Rmd ef6958a sq-96 2021-12-20 Start workflowr project.

Gene Expression Weights

Schizophrenia results link.

BMI results link.

Atrial Fibrillation - Heart Atrial Appendage Results link.

Atrial Fibrillation - Heart Left Ventricle Results link.

T2D - Liver Results link.

T2D - Pancreas Results link.

T2D - Adipose Visceral Omentum link.

T2D - Adipose Subcutaneous link.

Autism - Brain Cortex link.

Autism - Brain Spinal cord cervical c-1 link.

Autism - Brain Substantia nigra link.

Autism - Brain Putamen basal ganglia link.

Autism - Brain Nucleus accumbens basal ganglia link.

Autism - Brain Hypothalamus link.

Autism - Brain Hippocampus link.

Autism - Brain Frontal Cortex BA9 link.

Autism - Brain Cerebellum link.

Autism - Brain Cerebellar Hemisphere link.

Autism - Brain Caudate basal ganglia link.

Autism - Brain Anterior cingulate cortex BA24 link.

Autism - Brain Amygdala link.

Alternative Splicing Weights

BMI - Brain Cortex link.

BMI - Brain Spinal cord cervical c-1 link.

BMI - Brain Substantia nigra link.

BMI - Brain Putamen basal ganglia link.

BMI - Brain Nucleus accumbens basal ganglia link.

BMI - Brain Hypothalamus link.

BMI - Brain Hippocampus link.

BMI - Brain Frontal Cortex BA9 link.

BMI - Brain Cerebellum link.

BMI - Brain Cerebellar Hemisphere link.

BMI - Brain Caudate basal ganglia link.

BMI - Brain Anterior cingulate cortex BA24 link.

BMI - Brain Amygdala link.