Renzo bonifazi
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| alias ll='ls -lah --color=auto --classify --group-directories-first --time-style=long-iso' | |
| # alias ll='ls -lah --color=auto --classify --group-directories-first --time-style=long-iso --sort=time -r' | |
| alias diff-s='diff -s -wy --suppress-common-lines' | |
| alias squeue_comment="squeue --format='%18i %9P %8j %8u %2t %10M %6D %R %k'" |
bonifazi
/ count_animal_genotypes.awk
Created
June 29, 2023 14:54
Count 0,1,2,5 per animal genotypes
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| awk 'BEGIN { | |
| OFS = "," | |
| print "ID", 0, 1, 2, 5 | |
| } | |
| { | |
| for (i = 2; i <= NF; i++) { | |
| count[$1,$i]++ | |
| } | |
| vals[$1] = $1 | |
| } |
bonifazi
/ Plink2PCA.R
Last active
May 19, 2023 08:47
PCA for large datasets with Plink2 --pca approx
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| # First compute PCA files using Plink2 from the command line | |
| # Refer to https://www.cog-genomics.org/plink/2.0/strat#pca for how PCA approximation is done | |
| # As suggested in the link above, --maf is applied for variants below 0.01 | |
| # Plink2 command line is: | |
| # plink2 --cow --bfile <mybfile> --keep-allele-order --maf 0.01 --pca approx | |
| ######### plot in R ################ | |
| # Output: a 4 pages pdf file with: pages 1 to 3 are scatterplots of PCx vs PCx (with PCx from 1 to 3), page 4 is a 3D scatterplot of the first 3 PCs. | |
| pacman::p_load(dplyr, data.table, ggplot2, scatterplot3d) | |
| pca_res <- fread(file = "plink2.eigenvec") |
bonifazi
/ nested_list_to_dataframe.R
Last active
May 10, 2023 12:21
Convert nested list to dataframe quickly
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| pacman::p_load(Hmisc, rrapply) | |
| # loop variables | |
| scenarios <- c("scenario1", "scenario2") | |
| groups <- c("grp1", "grp2", "grp3", "grp4") | |
| # create two lists, one for the plots and one for the statistics only | |
| ALL_stats <- list() | |
| ALL_plots <- list() | |
| for(scenario in scenarios){ |
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| # different (similar) ways to check and load pkgs in R | |
| # method 1 | |
| check_pkgs <- function(pkg_list){ | |
| for(pkg in pkg_list) { | |
| if(!require(pkg, character.only = T)){ | |
| stop('Please install the ', pkg, ' package, using "install.packages(', pkg, ')"', call. = F) | |
| } | |
| } | |
| } | |
| check_pkgs(pkg_list = c("asserththat", "ggplot2")) |
bonifazi
/ Accompanying README.md example
Last active
March 27, 2025 10:45
Initiate a project structure
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| # Project_name_WP1 | |
| Project_name project, WP1, [other details]. | |
| ## Project structure | |
| Project structure is initiated with `init_project.sh.` | |
| These are the main directories: |
bonifazi
/ Template_Rscript.R
Last active
March 31, 2023 05:25
Rscript for command line execution and --flagged arguments checks
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| #!/usr/bin/env Rscript | |
| # | |
| # Purpose: what this script does. | |
| # Author: Renzo Bonifazi - dd-mm-yyyy | |
| # Usage: | |
| # # Rscript --vanilla myscript.R --file my_path/myfile.csv --output myoutput.csv | |
| # | |
| # Example: | |
| # # Rscript --vanilla Make_pedigree.R --file Renzo/Documents/file.csv --output Output.csv | |
| # |
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| # grep a string in multiple file names and include subdirectories | |
| grep --include 'file1.txt' --include 'file2.txt' -rn --ignore-case TITLE directory1 directory2 |