get_intervals: Retrieve the genomic locations of all genes in a given read...

In ferygood/TEffectR_yao:

Description

This function is used to retrieve the genomic locations of all genes in a given read count matrix by the user. Row names of the expression matrix must be one of the following: (i) official gene symbol, (ii) Ensembl gene or (iii) transcript ID. The output of this function is utilized while determining distance between genes and TEs.

Usage

get_intervals(x, assembly, ID.type, URL)

Arguments

x	a list of gene symbols, gene IDs or transcript IDs.
assembly	It is a character string that refers to the assembly of interest.
ID.type	It is a character string that refers to the ID type of interest. (ensembl_gene_name, ensemble_gene_id, ensemble_transcript_id).
URL	It is a character string that refers to the appropriate version of Ensembl database: http://www.ensembl.org/index.html.

See Also

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Examples

#Retrieve genomic position of genes.
TEffectR::get_intervals(x = rownames(gene.counts), assembly="hg38", ID.type = "ensembl_gene_id", URL="dec2014.archive.ensembl.org")

ferygood/TEffectR_yao documentation built on Jan. 1, 2021, 1:20 a.m.