Author: Arianna Rigamonti
GenesPackage is an R package that provides a structured representation of different types of genes. It includes methods for creating, manipulating, and accessing information related to various gene classes, such as protein-coding genes, lncRNA genes, and microRNA genes.
This package is developed as part of the Scientific Programming course project.
- Creation of gene objects: Define different gene types, including lncRNAs, microRNAs, piRNAs, and more.
- Gene information retrieval: Access attributes like gene symbol, description, chromosome location, and product.
- Gene modification: Update attributes dynamically within an R session.
- Integration with GenomicRanges: Utilize
GRangesobjects for genomic coordinate representation.
To install the package from source, use the following command:
# Install from local tar.gz file
install.packages("GenesPackage_0.1.0.tar.gz", repos = NULL, type = "source")
# Load the package
library(GenesPackage)- Creating a Generic Gene Object
library(GenomicRanges)
# Define genomic coordinates
gr <- GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end = 1000))
# Create a generic gene object
gene <- createGene(ID = 1L, symbol = "SYMBOL", name = "Gene Name",
description = "Description", chr = "chr1", start = 1,
end = 1000, strand = "+", product = list())
# Display gene information
gene- Creating an lncRNA Gene Object
lncrna_gene <- createLncRNAGene(ID = 2L, symbol = "SYMBOL_LNC", name = "LncRNA Name",
description = "LncRNA Description", chr = "chr1",
start = 1, end = 1000, strand = "+",
product = list(), lncRNAID = "lncrna1",
RNASequence = "RNA_SEQUENCE")
lncrna_gene- Retrieving Gene Attributes
getID(gene) # Get gene ID
getSymbol(gene) # Get gene symbol
getName(gene) # Get gene name
getDescription(gene) # Get gene description
getStructure(gene) # Get genomic coordinates- Modifying Gene Attributes
setSymbol(gene) <- "NEW_SYMBOL"
setName(gene) <- "New Gene Name"
setDescription(gene) <- "Updated Description"- R version: 4.4.1 or later
- Required packages: GenomicRanges, IRanges, S4Vectors, BiocGenerics
To install dependencies:
install.packages(c("GenomicRanges", "IRanges", "S4Vectors", "BiocGenerics"), dependencies = TRUE)