This function reads and converts Bismark's
'genome wide cytosine report' and 'coverage' into a
data.frames (one per chromosome) to a format compatible
with SOMNiBUS' main functions
formatFromBismark(..., verbose = TRUE)
logical indicates the level of information provided by the algorithm during the process. The default value is TRUE.
This function returns a
data.frames (one per
data.frame contains rows as individual CpGs
appearing in all the samples. The first 4 columns contain the information of
Meth_Counts (methylated counts),
Total_Counts (read depths),
Position (Genomic position for the CpG site) and
ID (sample ID).
The additional information (such as disease status, sex, age) extracted from
the BSseq object are listed in column 5 and onwards and will be considered
as covariate information by SOMNiBUS algorithms.
read.bismark for parsing output from the Bismark alignment suite.
Other Parsing functions:
infile <- system.file("extdata/test_data.fastq_bismark.bismark.cov.gz", package = "bsseq") dat <- formatFromBismark(infile, verbose = FALSE)
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