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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)
}
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