report: Generates an inclusive report on methylation analysis

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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.