summary {MACPET} | R Documentation |
Different summary methods for the classes in the
MACPET
package.
## S3 method for class 'PSelf' summary(object, ...) ## S3 method for class 'PSFit' summary(object, threshold = NULL, ...) ## S3 method for class 'PIntra' summary(object, heatmap = FALSE, ...) ## S3 method for class 'PInter' summary(object, heatmap = FALSE, ...)
object |
An object of correct class used to create different summaries. |
... |
Further arguments to be passed to the summary function. |
threshold |
A numeric representing the FDR cutoff for summarizing singificant peaks, if NULL the summary is based on all the peaks found. |
heatmap |
TRUE or FALSE indicating whether the user wants to plot a heat-map plot for the Intra/Inter-chromosomal PET counts within chromosomes or between different chromosomes. |
A summary of the object
and a heat-map plot depending on the
class of the input.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.
#load Self-ligated data: (class=PSelf) load(system.file('extdata', 'MACPET_pselfData.rda', package = 'MACPET')) class(MACPET_pselfData) summary(MACPET_pselfData) #load Self-ligated data: (class=PSFit) load(system.file('extdata', 'MACPET_psfitData.rda', package = 'MACPET')) class(MACPET_psfitData) summary(MACPET_psfitData) summary(MACPET_psfitData,threshold=1e-5) #load Intra-chromosomal data: (class=PIntra) load(system.file('extdata', 'MACPET_pintraData.rda', package = 'MACPET')) class(MACPET_pintraData) summary(MACPET_pintraData) requireNamespace('ggplot2') requireNamespace('reshape2') summary(MACPET_pintraData,heatmap=TRUE)#sample data, not good heatmap plot. #load Inter-chromosomal data: (class=PInter) load(system.file('extdata', 'MACPET_pinterData.rda', package = 'MACPET')) class(MACPET_pinterData) summary(MACPET_pinterData) requireNamespace('ggplot2') requireNamespace('reshape2') summary(MACPET_pinterData,heatmap=TRUE)#sample data, not good heatmap plot.