man/ligandReceptorTest.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ligandReceptor_analysis.R
 \name{ligandReceptorTest}
 \alias{ligandReceptorTest}
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 \title{ligandReceptorTest}
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 \usage{
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 ligandReceptorTest(
   sce,
   ligandReceptor_list,
   cluster,
   RNA_exprs_value = "minMax",
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   use_alt_exp = TRUE,
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   altExp_name = "ADT",
   altExp_exprs_value = "zi_minMax",
   num_permute = 1000,
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   p_sig = 0.05
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 )
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 }
 \arguments{
 \item{sce}{A singlecellexperiment object}
 
 \item{ligandReceptor_list}{A data.frame indicates the ligand receptor list}
 
 \item{cluster}{A vector indicates the cluster results}
 
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 \item{RNA_exprs_value}{A character indicates which expression value
 for RNA in assayNames is used.}
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 \item{use_alt_exp}{A logical vector indicates whether receptors
 expression will use alternative expression matrix to quantify.}
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 \item{altExp_name}{A character indicates which expression matrix is used.
 by default is ADT .}
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 \item{altExp_exprs_value}{A character indicates which expression value
 in assayNames is used.}
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 \item{num_permute}{Number of permutation.}
 
 \item{p_sig}{A numeric indicates threshold of the pvalue significance}
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 }
 \value{
 A SingleCellExperiment object with ligand receptor results
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 }
 \description{
 A function to perform ligand receptor analysis
 }
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 \examples{
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 data(lr_pair_subset, package = "CiteFuse")
 data(sce_control_subset, package = "CiteFuse")
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 sce_control_subset <- normaliseExprs(sce = sce_control_subset,
 altExp_name = "ADT",
 transform = "zi_minMax")
 
 sce_control_subset <- normaliseExprs(sce = sce_control_subset,
                               altExp_name = "none",
                               exprs_value = "logcounts",
                               transform = "minMax")
 
 sce_control_subset <- ligandReceptorTest(sce = sce_control_subset,
                                   ligandReceptor_list = lr_pair_subset,
                                   cluster = sce_control_subset$SNF_W_louvain,
                                   RNA_exprs_value = "minMax",
                                   use_alt_exp = TRUE,
                                   altExp_name = "ADT",
                                   altExp_exprs_value = "zi_minMax",
                                   num_permute = 100)
 }