compare {RNAmodR} | R Documentation |
To compare data of different samples, a
ModifierSet
can be used. To select the data
alongside the transcripts and their positions a
GRanges
or a
GRangesList
needs to be provided.
In case of a GRanges
object, the parent column must match the
transcript names as defined by the out put of ranges(x)
, whereas in
case of a GRangesList
the element names must match the transcript
names.
compare(x, name, pos = 1L, ...) compareByCoord(x, coord, ...) plotCompare(x, name, pos = 1L, normalize, ...) plotCompareByCoord(x, coord, normalize, ...) ## S4 method for signature 'ModifierSet' compare(x, name, pos = 1L, normalize, ...) ## S4 method for signature 'ModifierSet,GRanges' compareByCoord(x, coord, normalize, ...) ## S4 method for signature 'ModifierSet,GRangesList' compareByCoord(x, coord, normalize, ...) ## S4 method for signature 'ModifierSet' plotCompare(x, name, pos = 1L, normalize, ...) ## S4 method for signature 'ModifierSet,GRanges' plotCompareByCoord(x, coord, normalize, ...) ## S4 method for signature 'ModifierSet,GRangesList' plotCompareByCoord(x, coord, normalize, ...)
x |
a |
name |
Only for |
pos |
Only for |
... |
optional parameters:
|
coord |
coordinates of position to subset to. Either a |
normalize |
either a single logical or character value. If it is a
character, it must match one of the names in the |
compareByCoord
returns a
DataFrame
and
plotCompareByCoord
returns a ggplot
object, which can be
modified further. The DataFrame
contains columns per sample as well
as the columns names
, positions
and mod
incorporated
from the coord
input. If coord
contains a column
Activity
this is included in the results as well.
data(msi,package="RNAmodR") # constructing a GRanges obejct to mark positive positions mod <- modifications(msi) coord <- unique(unlist(mod)) coord$score <- NULL coord$sd <- NULL # return a DataFrame compareByCoord(msi,coord) # plot the comparison as a heatmap plotCompareByCoord(msi,coord)