| cellCellReport {scTensor} | R Documentation |
The result is saved as HTML report which contains with multiple files.
cellCellReport(sce, reducedDimNames,
out.dir=tempdir(), html.open=FALSE,
title="The result of scTensor",
author="The person who runs this script", assayNames = "counts", thr=100,
top="full", p=0.05, upper=20,
goenrich=TRUE, meshenrich=TRUE, reactomeenrich=TRUE,
doenrich=TRUE, ncgenrich=TRUE, dgnenrich=TRUE)
sce |
A object generated by instantization of SingleCellExperiment-class. |
reducedDimNames |
The name of two-dimentional data saved in reducedDimNames slot of SingleCellExperiment object. |
out.dir |
The output directory for saving HTML report (out.dir: tempdir()). |
html.open |
Whether the result of HTML report is opened when the calculation is finished (Default: FALSE). |
title |
The title of HTML report (Default: "The result of scTensor"). |
author |
The author of HTML report (Default: "The person who runs this script"). |
assayNames |
The unit of gene expression for using scTensor (e.g. normcounts, cpm...etc) (Default: "counts"). |
thr |
The threshold for selection of top pecentage of core tensor elements (Default: 100 (1 to 100)). |
top |
top genes in each (*,*,*)-pattern which are selected and summarized in the report (Default: "full") |
p |
The threshold of p-value of the enrichment analysis (Default: 1E-2) |
upper |
The maxium number of HTML reports generates (Default: 20) |
goenrich |
Whether GO-Enrichment analysis is performed (Default: TRUE) |
meshenrich |
Whether MeSH-Enrichment analysis is performed (Default: TRUE) |
reactomeenrich |
Whether Reactome-Enrichment analysis is performed (Default: TRUE) |
doenrich |
Whether DO-Enrichment analysis is performed (Default: TRUE) |
ncgenrich |
Whether NCG-Enrichment analysis is performed (Default: TRUE) |
dgnenrich |
Whether DGN-Enrichment analysis is performed (Default: TRUE) |
The result is saved as HTML report which contains with multiple files.
Koki Tsuyuzaki
if(interactive()){
# Package Loading
library("SingleCellExperiment")
library("LRBase.Hsa.eg.db")
library("MeSH.Hsa.eg.db")
# Data Loading
data(GermMale)
data(labelGermMale)
data(tsneGermMale)
# SingleCellExperiment Object
sce <- SingleCellExperiment(assays=list(counts = GermMale))
reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y)
# User's Original Normalization Function
CPMED <- function(input){
libsize <- colSums(input)
median(libsize) * t(t(input) / libsize)
}
# Normalization
normcounts(sce) <- log10(CPMED(counts(sce)) + 1)
# Registration of required information into metadata(sce)
cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale))
# Rank Estimation
rks <- cellCellRanks(sce, assayNames="normcounts")
# CCI Tensor Decomposition
cellCellDecomp(sce, ranks=rks$selected, assayNames="normcounts")
# HTML Report
cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts",
title="Cell-cell interaction within Germline_Male, GSE86146",
author="Koki Tsuyuzaki", html.open=TRUE, upper=2,
goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE,
doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE)
if(.Device == "quartz"){
dev.off()
}
}