Description Usage Arguments Value Examples
This function uses most of the functions in this package to generate a report for the user
1 2 |
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 |
Report will be an html file
1 2 3 4 5 6 | 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)
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