DotBracketDataFrame {Structstrings} | R Documentation |
The DotBracketDataFrame
object is derived from the
DataFrame
class. The
DotBracketDataFrameList
is implemented analogous, which is also
available as CompressedSplitDotBracketDataFrameList
. Since the names
are quite long, the following short cut functions are available for object
creation: DBDF
, DBDFL
and SDBDFL
.
The DotBracketDataFrame
can only contain 5 columns, which are named
pos
, forward
, reverse
, character
and base
.
The last two columns are optional. The type of the first three has to be
integer
, whereas the fourth is a character
and fifth is a
XStringSet
column.
Upon creation and modification, the validity of the contained base pairing information is checked. If the information is not correct, an error is thrown.
DotBracketDataFrame(...) DBDF(...) DotBracketDataFrameList(...) DBDFL(...) SplitDotBracketDataFrameList(..., compress = TRUE, cbindArgs = FALSE) SDBDFL(..., compress = TRUE, cbindArgs = FALSE)
... |
for |
compress |
If |
cbindArgs |
If |
a DotBracketDataFrame*
object.
# Manual creation df <- DataFrame(pos = c(1,2,3,4,5,6), forward = c(6,5,0,0,2,1), reverse = c(1,2,0,0,5,6)) # Either works dbdf <- as(df,"DotBracketDataFrame") dbdf <- DotBracketDataFrame(df) # With multiple input DataFrames a SplitDotBracketDataFrameList is returned dbdfl <- DotBracketDataFrame(df,df,df,df) # Creation from a DotBracketString object is probably more common data("dbs", package = "Structstrings", envir = environment()) dbdfl <- getBasePairing(dbs) # Elements are returned as DotBracketDataFrames dbdfl[[1]]