rgumbo

Copyright 2022 Marcello Del Corvo. Licensed under the MIT license.

Gumbo, like any other soup, is a mixture of different ingredients. This one in particular is made with a dark roux, vegetables, chicken, sausage, shrimp and served over rice. Except that instead of tasty food and fresh ingredients, rgumbo provides you with R functions.

This package is a result of me constantly breaking the DRY principle by copy-and-pasting functions from old projects into new ones. Hence, the functions in rgumbo do not have a single common topic, but they are all either related to manipulating genomic data or general productivity utilities.

This package has several functions that can prove to be useful and time-saving if you happen to need to perform one of the tasks implemented by rgumbo.

Installation

rgumbo is currently only available through GitHub and can be downloaded easily using devtools.

# install.packages("devtools")
devtools::install_github("mdelcorvo/rgumbo")

Getting started

There are many different usecases for rgumbo. See the overview vignette

browseVignettes("rgumbo")
vignette("overview", "rgumbo")

Alternatively, see the help file for any specific function for a complete detailed explanation of the function. For example ?rgumbo::LiftoverVcf.

Below is a very short introduction to the functions in rgumbo. You need to load the package first. library("rgumbo").

usePackage() function: check, install and load all required packages at one

Function to automatically check, install and load all required packages from both CRAN and Bioconductor repositories.

usePackage(pkgs = c('data.table','purrr','clusterProfiler'))

LiftoverVcf() function: lifts over a VCF file from one genome build to another

It produces a properly headered, sorted and compressed VCF in one go.

LiftoverVcf(vcf,output,from="hg38",to="hg19")

hgLiftOver() function: lifts over a bed-like files from one genome build to another

Converts genome coordinates between assemblies in a bed-like dataframe with chromosome number, start and (eventually) end position.

hgLiftOver(bed,from="hg38",to="hg19")

splitBed() function: split bed files by chunks, by number of rows for each chromosome or by chromosome.

Function to split bed files by chunks, by number of rows for each chromosome or by chromosome. File sizes may be variable.

splitBed<-function(bed,n,chrOnly=F,prefix=T,writeBed=F,verbose=T)

SnpEff() function: convert a SnpEff-based annotated vcf into a readable file

Function to make the SnpEff-based vcf readable by extracting the functional annotation and splitting each gene transcript into single rows.

SnpEff(vcf,modifier=F,amino=F,rm_dup=T)

HighCovBam() function: find high coverage regions in a bam file

Function to find and retrieve regions from a bam file based on a specific coverage cutoff.

HighCovBam(bam,cutoff=100,width=500)