https://github.com/m-osky/r-analysis

Some R scripts I wrote to analyse my data.
https://github.com/m-osky/r-analysis

Last synced: 18 days ago
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Some R scripts I wrote to analyse my data.

• Host: GitHub
• URL: https://github.com/m-osky/r-analysis
• Owner: M-Osky
• Created: 2017-10-02T10:20:58.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2021-09-06T12:12:38.000Z (over 3 years ago)
• Last Synced: 2023-12-04T14:57:58.356Z (about 1 year ago)
• Language: R
• Homepage:
• Size: 161 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# R ANALYSIS

Some short R scripts I wrote to analyse my data.

This is just a sample of some of the bioestatistics work I do with R either for our own research or for the students.

- The scripts done to be run in desktop R have some lines on the top describing the analysis, options and input file

- The scripts done to be run from command line (unix) have their own help information with the flag --help

# Short description

- HWtest - Analysis per population of loci out of Hardy-Weinberg equilibrium, filter out according to a p-value and percentage.

- LDA - Incomplete Linear Discriminant Analysis script, it works but needs to be adjusted and annotated properly for each case, still could be useful for some people starting

- Normality - test normality in multiple files and variables, plots distributions and tests different data transformation

- parametric tests (ANOVA) - Useful script when doing exploratory analysis of multiple files, we use it to check if the same variables behave similarly in different datasets

- Plot Fst Matrix - Plot per population pair-wise Fst hemimatrices (tested with Stampp package outputs)

- Plot Manhattan Fst - Quick script to plot per-locus Fst pair-wise values from populations (Stacks) output

- Pst_mcmc - Pst as an aproximationn to Qst (phenotypic distance) and comparison with Fst using Bayesian GLMM approach. [command line version]

- Pst_mcmc - Pst as an aproximationn to Qst (phenotypic distance) and comparison with Fst using Bayesian GLMM approach. [desktop version]

- Run and Plot RDA - not a ready to use script, needs better anotation and to be adjusted for each input file and option.

- average SD - Quick script that will output a table of summary statistics (quartiles, average, SD, etc.) from multiple files 

- basicgen Fst - Calculates pairwise Fst values with confidence intervals and p-values [command line version]

- basicgen diverindex - Calculates various allelic diversity indexes using hierfsts, diveRsity and dartR, outputs a table per population [command line version] 

- pairLDboxplot - categorize plink LD r-squared table in distance (kb) groups, useful to run in server in order to save time [command line version]

- pairLDdist - get summary tables from the scaffold sizes, distance, number of loci and LD from Plink LD analysis output, useful to run it in the server to save time [command line version]

- pairLDdist_windows - if your computer is fast enough skip the command line version of the script and directly calculate and plot from desktop R

- regression ressiduals - calculate linear and quadratic regression from multiple files, save plots, residuals, and summary table

# I'll be adding more complex scripts here once they are ready to be used by anyone (properly annotated and more broad options)