Convert Ensembles Version IDs & TCGA Version IDs to Genes in Bulk Expression Data

Preprocess bulk expression data: convert Ensembles version IDs and TCGA version IDs to genes. NA values are replaced with unknown_k format (k stands for the position of the NA value in the row).

Usage

SymbolConvert(
  data,
  unknown_format = "unknown_{k}",
  genome_build = c("hg38", "hg19", "mm10", "mm9"),
  verbose = SigBridgeRUtils::getFuncOption("verbose"),
  ...
)

Arguments

data

bulk expression data (matrix or data.frame)

unknown_format

A glue pattern containing {k} for replace the NA value during conversion. k must be wrapped in curly braces, stands for the position of the NA value in the row. Default: "unknown_{k}".

genome_build

Genome build of the data. Default: "hg38".

verbose

Whether to print verbose messages. Default: TRUE.

...

No usage