View source: R/filter_nonorthologs.R
filter_nonorthologs | R Documentation |
filter_nonorthologs
Takes the filenames of CellTypeData files,
loads them, drops any genes which don't have a 1:1 orthologs with humans,
and then convert the gene to human orthologs.
The new files are then saved to disk, appending
'_orthologs' to the file name.
filter_nonorthologs(
filenames,
input_species = NULL,
convert_nonhuman_genes = TRUE,
annot_levels = NULL,
suffix = "_orthologs",
method = "homologene",
non121_strategy = "drop_both_species",
verbose = TRUE,
...
)
filenames |
List of file names for sct_data saved as .rda files. |
input_species |
Which species the gene names in |
convert_nonhuman_genes |
Whether to convert the |
annot_levels |
[Optional] Names of each annotation level. |
suffix |
Suffix to add to the file name (right before .rda). |
method |
R package to use for gene mapping:
|
non121_strategy |
How to handle genes that don't have
1:1 mappings between
|
verbose |
Print messages. |
... |
Arguments passed on to
|
Note: This function replaces the original
filter_genes_without_1to1_homolog
function.
filter_genes_without_1to1_homolog
is
now a wrapper for filter_nonorthologs
.
List of the filtered CellTypeData file names.
# Load the single cell data
ctd <- ewceData::ctd()
tmp <- tempfile()
save(ctd, file = tmp)
fNames_ALLCELLS_orths <- EWCE::filter_nonorthologs(filenames = tmp)
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