Description Usage Arguments Details Value Examples
Obtain cell barcodes, feature names, and feature IDs of an ondisc_matrix
, metadata_ondisc_matrix
,
or multimodal_ondisc_matrix
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | get_feature_ids(x)
get_feature_names(x)
get_cell_barcodes(x)
## S4 method for signature 'ondisc_matrix'
get_feature_ids(x)
## S4 method for signature 'ondisc_matrix'
get_feature_names(x)
## S4 method for signature 'ondisc_matrix'
get_cell_barcodes(x)
## S4 method for signature 'metadata_ondisc_matrix'
get_feature_ids(x)
## S4 method for signature 'metadata_ondisc_matrix'
get_feature_names(x)
## S4 method for signature 'metadata_ondisc_matrix'
get_cell_barcodes(x)
## S4 method for signature 'multimodal_ondisc_matrix'
get_feature_ids(x)
## S4 method for signature 'multimodal_ondisc_matrix'
get_feature_names(x)
## S4 method for signature 'multimodal_ondisc_matrix'
get_cell_barcodes(x)
|
x |
an object of class |
The following functions can be used to obtain feature and cell identifiers:
get_cell_barcodes
: return the cell barcodes.
get_feature_names
: return the feature names.
get_feature_ids
: return the IDs of the features.
In general, these functions return a character vector containing the requested identifiers. When
get_feature_names
or get_feature_ids
is called on a multimodal_ondisc_matrix
, the function instead
returns a list containing the feature names and feature IDs, respectively, of the modalities contained
within the multimodal_ondisc_matrix
.
A character vector or list of character vectors containing the requested identifiers.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | # NOTE: You must create the RDS files "expressions.rds" and
# "perturbations.rds" to run this example. Navigate to the help file of
# "create_ondisc_matrix_from_mtx" (via ?create_ondisc_matrix_from_mtx),
# and execute both code blocks.
# ondisc_matrix
h5_fp <- paste0(tempdir(), "/expressions.h5")
if (file.exists(h5_fp)) {
odm <- ondisc_matrix(h5_file = h5_fp)
barcodes <- get_cell_barcodes(odm)
feature_names <- get_feature_names(odm)
feature_ids <- get_feature_ids(odm)
}
# metadata_ondic_matrix
expressions_fp <- paste0(tempdir(), "/expressions.rds")
if (file.exists(expressions_fp)) {
expressions <- readRDS(expressions_fp)
barcodes <- get_cell_barcodes(odm)
feature_names <- get_feature_names(odm)
feature_ids <- get_feature_ids(odm)
}
# multimodal_ondisc_matrix
expression_fp <- paste0(tempdir(), "/expressions.rds")
perturbations_fp <- paste0(tempdir(), "/perturbations.rds")
if (file.exists(expression_fp) && file.exists(perturbations_fp)) {
crispr_experiment <- multimodal_ondisc_matrix(list(expressions = readRDS(expression_fp),
perturbations = readRDS(perturbations_fp)))
barcodes <- get_cell_barcodes(crispr_experiment)
feature_ids <- get_feature_ids(crispr_experiment)
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.