Converts mouse gene symbols to human gene symbols in an expression dataset. Supports using either an online resource (Ensembl) or a local dataset for conversion.
Usage
mouse2human_eset(
eset,
source = c("local", "ensembl"),
is_matrix = TRUE,
column_of_symbol = NULL,
verbose = FALSE
)Arguments
- eset
Matrix or data frame. Expression matrix with genes in rows.
- source
Character. Data source for conversion: "ensembl" (online) or "local". Default is "ensembl". If Ensembl fails, use "local" which uses the internal `mus_human_gene_symbol` dataset.
- is_matrix
Logical. Whether `eset` is a matrix with gene symbols as row names. Default is `TRUE`. If `FALSE`, `column_of_symbol` must be specified.
- column_of_symbol
Character or `NULL`. Column name containing gene symbols if `eset` is not a matrix. Default is `NULL`.
- verbose
Logical. If `TRUE`, prints available Ensembl datasets. Default is `FALSE`.
Examples
# Create example mouse expression data
anno_gc_vm32 <- load_data("anno_gc_vm32")
num_rows <- 200
num_cols <- 10
sample_names <- paste0("Sample", 1:num_cols)
data <- matrix(runif(num_rows * num_cols), nrow = num_rows, ncol = num_cols)
rownames(data) <- anno_gc_vm32$symbol[1:200]
colnames(data) <- sample_names
# Convert using local database
human_data <- mouse2human_eset(data, source = "local", is_matrix = TRUE)
#> ℹ Row number of original eset: 200
#> ✔ 94% of probes in expression set were annotated
#> ℹ Found 1 duplicate symbol, using "mean" method
#> ℹ Row number after filtering duplicated gene symbol: 217