DotBracketDataFrame {Structstrings} | R Documentation |
The DotBracketDataFrame
and DotBracketDFrame
object is derived
from the DataFrame
and
DFrame
classes.
DotBracketDataFrame
implents the concept and can be used to implement
other backends than the in-memory one as done by DotBracketDFrame
.
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(..., row.names = NULL) DBDF(...) DotBracketDataFrameList(...) DBDFL(...) SplitDotBracketDataFrameList(..., compress = TRUE, cbindArgs = FALSE) SDBDFL(..., compress = TRUE, cbindArgs = FALSE)
... |
for |
row.names |
See |
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") dbdfl <- getBasePairing(dbs) # Elements are returned as DotBracketDataFrames dbdfl[[1]]