liana_bysample: Wrapper around 'liana_wrap' to run liana for each sample.

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Wrapper around 'liana_wrap' to run liana for each sample.

Description

Wrapper around 'liana_wrap' to run liana for each sample.

Usage

liana_bysample(
  sce,
  idents_col,
  sample_col,
  verbose = TRUE,
  inplace = TRUE,
  aggregate_how = NULL,
  ...
)

Arguments

idents_col	name of the cluster column
sample_col	name of the sample/context column
verbose	verbosity logical
inplace	logical (TRUE by default) if liana results are to be saved to the SingleCellExperiment object ('sce@metadata$liana_res')
aggregate_how	if running multiple methods (default), then one cal also choose to aggregate the CCC results by sample.
...	Arguments passed on to liana_wrap sce 'SingleCellExperiment' object or 'SeuratObject' method method(s) to be run via liana resource resource(s) to be used by the methods ('Consensus' by default), Use 'all' to run all 'human' resources in one go), or 'custom' to run liana_wrap with an appropriately formatted custom resource, passed via 'exernal_resource' external_resource external resource in OmniPath tibble format min_cells minimum cell per cell identity to be considered for analysis return_all whether to return all possible interactions. Any interaction with 'expr_prop' below the specific threshold will be assigned to the *worst* possible score in those that pass the threshold. For example, p-values from CellPhoneDB will be assigned to max(pvalue) - likely 1, and lr_means will be assigned to min(lr_means). Note that this applies only to the internal methods of liana. supp_columns any supplementary/additional columns which are to be returned by liana. Possibilities include: c("ligand.expr", "receptor.expr" "ligand.stat", "receptor.stat", "ligand.pval", "receptor.pval", "ligand.FDR", "receptor.FDR", etc) assay assay to be used by Seurat, by default set to 'NULL' and will use the DefaultAssay. .simplify if methods are run with only 1 resource, return a list of tibbles for each method (default), rather than a list of lists with method-resource combinations base Default to NULL (i.e. log2-transformation is assumed for SCE, and log-tranformation for Seurat). This is a requred step for the calculation of the logFC method - ensures that any other preprocessing of the counts is preserved. One could also pass 'NaN' if they wish to use the counts stored in the counts assay/slot, or any other number according to the base that was used for log-tranformation. cell.adj cell adjacency tibble/dataframe /w weights by which we will 'multiply' the relevant columns. Any cell pairs with a weights of 0 will be filtered out. Note that if working with LIANA's default methods, we suggest weights >= 0 & =< 1. This ensure that all methods' score will be meaningfully weighed without changing the interpretation of their scores, thus allow one to filter SCA, rank NATMI, etc.

Details

takes a Seurat/SCE object and runs LIANA by sample/condition. The key by which the samples are separated is build from the 'condition_col' and 'sample_col', separated by the 'key_sep'.

Value

If inplace is true returns a sce object with 'liana_res' in 'sce@metadata', else it returns a named list of tibble with liana results per sample.

saezlab/liana documentation built on Aug. 10, 2024, 8:14 a.m.