getLociGenes: Retrieve summary information of the genes in a locus

In otargen: Access Open Target Genetics

Retrieve summary information of the genes in a locus

Description

This function retrieves information for a specified region on a chromosome, including overlapping genes and their associated details such as ID, symbol, biotype, description, transcription start site (TSS), start position, end position, strand direction, and exons structure.

Usage

getLociGenes(chromosome, start, end)

Arguments

chromosome	Character: Chromosome number as a string.
start	Integer: Start position of the specified region on the chromosome.
end	Integer: End position of the specified region on the chromosome.

Value

Returns a tibble data frame of all the overlapping genes in the specified region with the following data structure:

• id: Character. ID of the gene.

• symbol: Character. Symbol of the gene.

• bioType: Character. Biotype of the gene.

• description: Character. Description of the gene.

• chromosome: Character. Chromosome of the gene.

• tss: Integer. Transcription start site of the gene.

• start: Integer. Start position of the gene.

• end: Integer. End position of the gene.

• fwdStrand: Logical. Strand direction of the gene.

• exons: List. List of exons of the gene.

Examples

## Not run: 
result <- get_genes(chromosome = "2", start = 239634984, end = 241634984)

## End(Not run)

otargen documentation built on Sept. 30, 2024, 9:43 a.m.