generateReport: generate a QC report in a html file

In liuqivandy/scRNABatchQC: a package for quality control of multiple single cell RNAseq data

Description

Generate a QC report by comparing technical and biological features across multiple scRNA-seq datasets

Usage

generateReport(
  sces,
  scesMerge,
  outputFile = "report.html",
  lineSize = 1,
  pointSize = 0.8
)

Arguments

sces	a list of SingleCellExperiment Objects; each object containing quality meta data for one single cell RNAseq dataset (results from Process_scRNAseq)
scesMerge	a SingleCellExperiment object generated by combining and comparing multiple single cell RNAseq datasets (results from Combine_scRNAseq)
outputFile	the name of the output file (default: report.html)
lineSize	float; the line size of figures in the generated report (default: 1)
pointSize	float; the point size of figures in the generated report (default: 0.8)

See Also

Process_scRNAseq Combine_scRNAseq

Examples

library(scRNABatchQC)
sces<-Process_scRNAseq(inputs=c("https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar1.csv.gz","https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar5.csv.gz"))
scesMerge <- Combine_scRNAseq(sces)
generateReport(sces,scesMerge)

liuqivandy/scRNABatchQC documentation built on March 24, 2021, 11:01 p.m.