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Addition of R script to compare CNV caller output #142

Merged
merged 20 commits into from
Oct 22, 2019
Merged

Addition of R script to compare CNV caller output #142

merged 20 commits into from
Oct 22, 2019

Commits on Oct 2, 2019

  1. Addition of R script to compare CNV caller output 

    - Plots were made using GenVisR and ggplot2
- Addition of custom functions script (sourced in plotting script)
    @cbethell
    cbethell committed Oct 2, 2019
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  2. Merge branch 'master' into cnv-comparison-plotting

    @cbethell
    cbethell authored Oct 2, 2019
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Commits on Oct 7, 2019

  1. Attempted to DRY up the code 

    - added a `read_in_cnv` function
- removed `set.seed()` as it seemed unnecessary
    @cbethell
    cbethell committed Oct 7, 2019
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  2. Merge remote-tracking branch 'origin/cnv-comparison-plotting' into cn… 

    …v-comparison-plotting
    @cbethell
    cbethell committed Oct 7, 2019
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  3. Updated branch

    @cbethell
    cbethell committed Oct 7, 2019
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  4. Removed set.seed 

    `set.seed` no longer seems to be necessary in this script
    @cbethell
    cbethell committed Oct 7, 2019
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Commits on Oct 8, 2019

  1. Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysis … 

    …into cnv-comparison-plotting
    @cbethell
    cbethell committed Oct 8, 2019
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  2. @cansav09 PR review suggested changes

    @cbethell
    cbethell committed Oct 8, 2019
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Commits on Oct 10, 2019

  1. Merge branch 'master' into cnv-comparison-plotting

    @cbethell
    cbethell authored Oct 10, 2019
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Commits on Oct 17, 2019

  1. Merge branch 'master' into cnv-comparison-plotting

    @cbethell
    cbethell authored Oct 17, 2019
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  2. @jashapiro PR review suggested changes 

    - removed the `plot_cnfreq` function from the functions script and implemented `GenVisR::cnFreq` function in the `01` script
- reordered the chromosome levels
    Chante Bethell committed Oct 17, 2019
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  3. - Converted chrom column vector into a true factor vector 

    - included `stringsAsFactors = FALSE` argument to `read.table` function
    Chante Bethell committed Oct 17, 2019
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  4. Revert GenVisR::cnFreq to plot_cn_freq change in 01 script 

    - re-ran plots
    Chante Bethell committed Oct 17, 2019
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  5. Install cowplot from cran

    Chante Bethell committed Oct 17, 2019
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Commits on Oct 21, 2019

  1. Merge branch 'master' into cnv-comparison-plotting

    @cbethell
    cbethell authored Oct 21, 2019
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  2. Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysis … 

    …into cnv-comparison-plotting
    @cbethell
    cbethell committed Oct 21, 2019
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  3. Merge branch 'cnv-comparison-plotting' of https://github.com/cbethell… 

    …/OpenPBTA-analysis into cnv-comparison-plotting
    @cbethell
    cbethell committed Oct 21, 2019
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  4. Converted R script into R notebook 

    - combined data.frames and used faceting to plot ggplots
    @cbethell
    cbethell committed Oct 21, 2019
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  5. Updated .circleci/config.yml

    @cbethell
    cbethell committed Oct 21, 2019
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Commits on Oct 22, 2019

  1. Renamed input in list in .Rmd file 

    - fixed spacing around `~` operator 
- fixed line spacing in `.Rmd` file
    @cbethell
    cbethell committed Oct 22, 2019
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