query_methy | R Documentation |
Query methylation data
query_methy(
x,
chr,
start,
end,
simplify = TRUE,
force = FALSE,
truncate = TRUE,
site_filter = getOption("NanoMethViz.site_filter", 3L)
)
x |
the NanoMethResults object or a path to the methylation data (tabix-bgzipped). |
chr |
the vector of chromosomes |
start |
the vector of start positions |
end |
the vector of end positions |
simplify |
whether returned results should be row-concatenated |
force |
whether to force empty output when query region 'chr' does not appear in data. Without 'force', an empty result indicates that the requested 'chr' appears in the data but no data overlaps with requested region, and an invalid 'chr' will cause an error. |
truncate |
when querying from ModBamFiles, whether or not to truncate returned results to only those within the specified region. Otherwise methylation data for entire reads overlapping the region will be returned. |
site_filter |
the minimum amount of coverage to report a site. This
filters the queried data such that any site with less than the filter is
not returned. The default is 1, which means that all sites are returned.
This option can be set globally using the |
The argument site_filter
can be set globally using the options(site_filter = ...)
command. The same data entry may appear multiple times in the output
if it overlaps multiple regions.
A table containing the data within the queried regions. If simplify is TRUE (default) then returns all data in a single table, otherwise returns a list of tables where each table is the data from one region.
nmr <- load_example_nanomethresult()
query_methy(methy(nmr), "chr7", 6703892, 6730431)
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