filter_genes_without_1to1_homolog — filter_genes_without_1to1

Deprecated function. Please use filter_nonorthologs instead.

filter_genes_without_1to1_homolog(
  filenames,
  input_species = "mouse",
  convert_nonhuman_genes = TRUE,
  annot_levels = NULL,
  suffix = "_orthologs",
  verbose = TRUE
)

Arguments

filenames: List of file names for sct_data saved as .rda files.
input_species: Which species the gene names in exp come from.
convert_nonhuman_genes: Whether to convert the exp row names to human gene names.
annot_levels: [Optional] Names of each annotation level.
suffix: Suffix to add to the file name (right before .rda).
verbose: Print messages.

Value

List of the filtered CellTypeData file names.

Details

Note: This function replaces the original filter_genes_without_1to1_homolog function. filter_genes_without_1to1_homolog is now a wrapper for filter_nonorthologs.

Examples

# Load the single cell data
ctd <- ewceData::ctd()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
tmp <- tempfile()
save(ctd, file = tmp)
fNames_ALLCELLS_orths <- EWCE::filter_nonorthologs(filenames = tmp)
#> No input_species provided. Setting to 'mouse'
#> + Processing level 1 ...
#> Processing mean_exp
#> Processing median_exp
#> Processing specificity
#> Processing median_specificity
#> Processing specificity_quantiles
#> + Processing level 2 ...
#> Processing mean_exp
#> Processing median_exp
#> Processing specificity
#> Processing median_specificity
#> Processing specificity_quantiles