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", thr=40, top="full", p=0.05)
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"). |
thr |
The threshold for selection of top pecentage of core tensor elements (Default: 40 (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) |
The result is saved as HTML report which contains with multiple files.
Koki Tsuyuzaki
if(interactive()){ library("SingleCellExperiment") library("LRBase.Hsa.eg.db") library("MeSH.Hsa.eg.db") source("scTensor/R/scTensor-internal.R") data(GermMale) data(labelGermMale) data(tsneGermMale) sce <- SingleCellExperiment(assays=list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y) cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) rks <- cellCellRanks(sce) cellCellDecomp(sce, ranks=rks$selected) cellCellReport(sce, reducedDimNames="TSNE", title="Cell-cell interaction within Germline_Male, GSE86146", author="Koki Tsuyuzaki", thr=30, html.open=TRUE) }