Description Usage Arguments See Also Examples
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.
1 | get_intervals(x, assembly, ID.type, URL)
|
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. |
1 2 | #Retrieve genomic position of genes.
TEffectR::get_intervals(x = rownames(gene.counts), assembly="hg38", ID.type = "ensembl_gene_id", URL="dec2014.archive.ensembl.org")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.