report {scmeth} | R Documentation |
This function uses most of the functions in this package to generate a report for the user
report(bsObj, outdirectory, organism, genome, mbiasDir = NULL, subSample = 1e+06, offset = 50000, small = FALSE)
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
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)