MD helper functions

Lightweight version of the MDmisc R package containing various helper functions for computational genomics research. Old version

Installation

if (!require('devtools')) install.packages('devtools')
devtools::install_github('mdozmorov/MDmisc')

Functions

• gene_filter - Removes low expression and low variability genes from a gene expression matrix. Filters by the proportion of expressed genes, and/or min expression difference.

• pca_func - PCA plot with groups wrapped into ellipses. pca_func(iris[, 1:3], groups = iris$Species, title = "Iris")

• round_df - Round all columns with numerical values in a data frame

• unembed.R - Splits rows based on values embedded in a column based on a separator. E.g. one row with "ABC11 /// BCD22" variable in a column in will be split into two separate entries (" /// " separator), creating two ABC11 and BCD22 rows with other values equal to the original row

Depreciated

• ipak - Unified installer for CRAN, Bioconductor, and GitHub packages. Depreciated, use BiocManager::install(c("tidyverse", "blogdown", "xaringan", "xaringanthemer")) to install packages from Bioconductor, CRAN, and GitHub.

• save_res - A function to save a data frame or a matrix into an Excel file. Legacy function for compatibility with old code. Depreciated, use writexl::write_xlsx()

Notes

How to remove all user installed packages in R

# create a list of all installed packages
ip <- as.data.frame(installed.packages())
head(ip)
# if you use MRO, make sure that no packages in this library will be removed
ip <- subset(ip, !grepl("MRO", ip$LibPath))
# we don't want to remove base or recommended packages either\
ip <- ip[!(ip[,"Priority"] %in% c("base", "recommended")),]
# determine the library where the packages are installed
path.lib <- unique(ip$LibPath)
# create a vector with all the names of the packages you want to remove
pkgs.to.remove <- ip[,1]
head(pkgs.to.remove)
# remove the packages
sapply(pkgs.to.remove, remove.packages, lib = path.lib)