Get Gene CN and Expression. — get_gene_cn_and

Get the copy number and expression for a single gene.

get_gene_cn_and_expression(gene_symbol, ensembl_id, this_seq_type = "genome")

Arguments

gene_symbol: One or more gene symbols. Should match the values in a maf file.
ensembl_id: One or more ensembl gene IDs. Only one of hugo_symbols or ensembl_gene_ids may be used.
this_seq_type: Seq type for returned CN segments. One of "genome" (default) or "capture".

Value

A data frame with copy number information and gene expressions.

Details

This function works well with both Hugo Symbols and Ensembl Gene IDs. It's also possible to specify more than one gene.

Examples

MYC_cn_expression = get_gene_cn_and_expression("MYC")
#> [1] "grep -w -F -e Hugo_Symbol -e MYC /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv"