subsetByCoord {RNAmodR} | R Documentation |
SequenceData
, SequenceDataSet
,
SequenceDataList
, Modifier
or ModifierSet
object.With the subsetByCoord
function data from a SequenceData
,
SequenceDataSet
, SequenceDataList
, Modifier
or
ModifierSet
object can be subset to positions as defined in
coord
.
If coord
contains a column mod
and x
is a
Modifier
object, it will be filtered to identifiers matching the
modType
of x
. To disable this
behaviour remove the column mod
from coord
or set type =
NA
labelByCoord
functions similarly. It will return a
SplitDataFrameList
, which matches the dimensions of the aggregated
data plus the labels
column, which contains logical values to indicate
selected positions.
subsetByCoord(x, coord, ...) labelByCoord(x, coord, ...) ## S4 method for signature 'Modifier,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'Modifier,GRangesList' subsetByCoord(x, coord, ...) ## S4 method for signature 'ModifierSet' subset(x, name, pos = 1L, ...) ## S4 method for signature 'ModifierSet,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'ModifierSet,GRangesList' subsetByCoord(x, coord, ...) ## S4 method for signature 'Modifier,GRanges' labelByCoord(x, coord, ...) ## S4 method for signature 'Modifier,GRangesList' labelByCoord(x, coord, ...) ## S4 method for signature 'ModifierSet,GRanges' labelByCoord(x, coord, ...) ## S4 method for signature 'ModifierSet,GRangesList' labelByCoord(x, coord, ...) ## S4 method for signature 'SplitDataFrameList,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceData' subset(x, name, pos = 1L, ...) ## S4 method for signature 'SequenceData,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceData,GRangesList' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataSet' subset(x, name, pos = 1L, ...) ## S4 method for signature 'SequenceDataSet,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataSet,GRangesList' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataList' subset(x, name, pos = 1L, ...) ## S4 method for signature 'SequenceDataList,GRanges' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataList,GRangesList' subsetByCoord(x, coord, ...) ## S4 method for signature 'SequenceData,GRanges' labelByCoord(x, coord, ...) ## S4 method for signature 'SequenceData,GRangesList' labelByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataSet,GRanges' labelByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataSet,GRangesList' labelByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataList,GRanges' labelByCoord(x, coord, ...) ## S4 method for signature 'SequenceDataList,GRangesList' labelByCoord(x, coord, ...)
x |
a |
coord |
coordinates of position to subset to. Either a |
... |
Optional parameters:
|
name |
Optional: Limit results to one specific transcript. |
pos |
Optional: Limit results to a specific position. |
If 'x' is a
SequenceData
or
Modifier
: a SplitDataFrameList
with elments per transcript.
SequenceDataSet
,
SequenceDataList
or
ModifierSet
: a SimpleList
of
SplitDataFrameList
with elments per transcript.
data(msi,package="RNAmodR") mod <- modifications(msi) coord <- unique(unlist(mod)) coord$score <- NULL coord$sd <- NULL subsetByCoord(msi,coord)