report: Generates an inclusive report on methylation analysis

In aryeelab/scmeth: Functions to conduct quality control analysis in methylation data

Description

This function uses most of the functions in this package to generate a report for the user

Usage

report(bsObj, outdirectory, organism, genome, mbiasDir = NULL,
  subSample = 1e+06, offset = 50000, small = FALSE)

Arguments

bsObj	bsseq object
outdirectory	name of the output directory where the report will be saved
organism	scientific name of the organism of interest, e.g. Mmusculus or Hsapiens
genome	reference alignment, e.g. mm10 or hg38 the report will have graphics on read information
mbiasDir	Optional argument to provide directory name that has the mbias files or the list of mbias files
subSample	number of CpGs to subsample Default value is 1000000.
offset	how many CpGs to offset when subsampling Default value is set to be 50000, i.e. first 50000 CpGs will be ignored in subsampling.
small	Indicator for a small dataset, cpg density is calculated more

Value

Report will be an html file

Examples

library(BSgenome.Hsapiens.NCBI.GRCh38)
directory <- system.file("extdata/bismark_data", package='scmeth')
bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
mbiasDirectory=system.file("extdata", package='scmeth')
outDir <- system.file(package='scmeth')
report(bs, outDir, Hsapiens, 'hg38', mbiasDir=mbiasDirectory, small=TRUE)

aryeelab/scmeth documentation built on June 15, 2019, 8:02 p.m.