liana_call: Wrapper Function to obtain scores via liana_pipe

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

Wrapper Function to obtain scores via liana_pipe

Description

Wrapper Function to obtain scores via liana_pipe

Usage

liana_call(method, lr_res, ...)

Arguments

method	name of the method to be called
lr_res	ligand-receptor DE results and other stats between clusters
...	Arguments passed on to liana_pipe sce SingleCellExperiment Object op_resource resource tibble obtained via liana::select_resource assay assay to be used ("RNA" by default) assay.type - the type of data to be used to calculate the means (logcounts by default), available options are: "counts" and "logcounts" verbose logical for verbosity 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. test.type String specifying the type of pairwise test to perform - a t-test with "t", a Wilcoxon rank sum test with "wilcox", or a binomial test with "binom". pval.type A string specifying how p-values are to be combined across pairwise comparisons for a given group/cluster. base base for conversion from log-tranformed ~CPM back to ~CPM.

Value

lr_res modified to be method-specific

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