Get Gene Expression. — get_gene

Get the expression for one or more genes for all GAMBL samples.

get_gene_expression(
  metadata,
  hugo_symbols,
  ensembl_gene_ids,
  join_with = "mrna",
  all_genes = FALSE,
  expression_data,
  from_flatfile = TRUE
)

Arguments

metadata: GAMBL metadata.
hugo_symbols: One or more gene symbols. Should match the values in a maf file.
ensembl_gene_ids: One or more ensembl gene IDs. Only one of hugo_symbols or ensembl_gene_ids may be used.
join_with: How to restrict cases for the join. Can be one of genome, mrna or "any".
all_genes: Set to TRUE to return the full expression data frame without any subsetting. Avoid this if you don't want to use tons of RAM.
expression_data: Optional argument to use an already loaded expression data frame (prevent function to re-load full df from flat file or database).
from_flatfile: Deprecated but left here for backwards compatibility.

Value

A data frame with gene expression.

Details

Effectively get gene expression for one or multiple genes for al GAMBL samples. This function can also take an already loaded expression matrix (expression_data) to prevent the user from having to load the full expression matrix if this function needs to be run in an interactive session. For examples and more info, refer to the parameter descriptions as wella s vignette examples.

Examples

MYC_expr = get_gene_expression(hugo_symbols = c("MYC"), join_with = "mrna")
#> [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"

#Read full expression values df (no subsetting on genes)
full_expression_df = get_gene_expression(all_genes = TRUE,
                                             join_with = "genome")
#> Warning: NAs produced by integer overflow
#> Error in vec_init(value, nrow * ncol): `n` must be a single number, not an integer `NA`.

#Use loaded df (in the previous step) to get expression values for IRF4 and MYC.
irf4_myc_expressions = get_gene_expression(hugo_symbols = c("IRF4", "MYC"),
                                               all_genes = FALSE,
                                               join_with = "genome",
                                               from_flatfile = FALSE,
                                               expression_data = full_expression_df)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': object 'full_expression_df' not found