View source: R/RCTDreplicates.R
run.CSIDE.replicates | R Documentation |
RCTD.replicates
objectIdentifies cell type specific differential expression (DE) as a function of the explanatory variable for each replicate. The design matrix contains an intercept column and a column of the explanatory variable. Uses maximum likelihood estimation to estimate DE and standard errors for each gene and each cell type. Selects genes with significant nonzero DE. Note: a minimum of three replicates are required for population mode.
run.CSIDE.replicates(
RCTD.replicates,
cell_types,
explanatory.variable.replicates = NULL,
X.replicates = NULL,
cell_type_threshold = 125,
gene_threshold = 5e-05,
doublet_mode = T,
weight_threshold = NULL,
sigma_gene = T,
PRECISION.THRESHOLD = 0.05,
cell_types_present = NULL,
fdr = 0.01,
population_de = F,
replicate_index = NULL,
normalize_expr = F,
test_genes_sig_individual = F,
de_mode = "single",
df = 15,
barcodes = NULL,
log_fc_thresh = 0.4,
test_error = F,
medv = 0.5,
params_to_test = NULL,
test_mode = "individual"
)
RCTD.replicates |
an |
cell_types |
the cell types used for CSIDE. Each cell type must occur
at least 'cell_type_threshold', as aggregated by |
explanatory.variable.replicates |
(only used for de_mode = single) a list of the named numeric vectors representing for each replicate the explanatory variable used for explaining differential expression in CSIDE.
Names of the vectors are the |
X.replicates |
(only used for de_mode = general) a list for each replicate of matrices containing the covariates for running CSIDE. The rownames represent pixel names and
should be a subset of the pixels in the |
cell_type_threshold |
(default 125) min occurence of number of cells for each cell type to be used, as aggregated by |
gene_threshold |
(default 5e-5) minimum average normalized expression required for selecting genes |
doublet_mode |
(default TRUE) if TRUE, uses RCTD doublet mode weights. Otherwise, uses RCTD full mode weights |
weight_threshold |
(default NULL) the threshold of total normalized weights across all cell types
in |
sigma_gene |
(default TRUE) if TRUE, fits gene specific overdispersion parameter. If FALSE, overdispersion parameter is same across all genes. |
PRECISION.THRESHOLD |
(default 0.05) for checking for convergence, the maximum parameter change per algorithm step |
cell_types_present |
cell types (a superset of 'cell_types') to be considered as occuring often enough to consider for gene expression contamination during the step filtering out marker genes of other cell types. |
fdr |
(default 0.01) false discovery rate for hypothesis testing |
population_de |
(default FALSE) whether population-level DE should be run (can also be run later using the |
replicate_index |
(default all replicates) integer list of replicate indices (subset of 1:N_replicates) to be run for CSIDE |
normalize_expr |
(default FALSE) if TRUE, constrains total gene expression to sum to 1 in each condition. |
test_genes_sig_individual |
(default FALSE) logical controlling whether on individual samples genes will be tested for significance. |
de_mode |
(default 'single', otherwise 'nonparam' or 'general') if 'single', calls |
df |
(default 15) for de_mode = nonparam, the degrees of freedom, or number of basis functions to be used in the model. |
barcodes |
for de_mode = nonparam, the barcodes, or pixel names, of the |
log_fc_thresh |
(default 0.4) the natural log fold change cutoff for differential expression |
test_error |
(default FALSE) if TRUE, first tests for error messages before running CSIDE. If set to TRUE, this can be used to quickly evaluate if CSIDE will run without error. |
medv |
(default 0.5) for single model, the cutoff value of explanatory.variable (after 0-1 normalization) for determining if enough pixels for each cell type have explanatory-variable greater than or less than this value (minimum cell_type_threshold/2 required). |
params_to_test: |
(default 2 for test_mode = 'individual', all parameters for test_mode = 'categorical'). An integer vector of parameter indices to test. For example c(1,4,5) would test only parameters corresponding to columns 1, 4, and 5 of the design matrix. |
an RCTD.replicates
object containing the results of the CSIDE algorithm. See RCTD.replicates
for documentation on the population_de_results
, population_sig_gene_list
, and population_sig_gene_df
objects.
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