plotInOutFeatures {TarSeqQC} | R Documentation |
plotInOutFeatures
allows the graphical exploration of the data
frame obtained using readFrequencies
. This data frame contains
information about the amount of reads mapped to the targeted regions and out of
them. This information is presented in rows, one for each chromosome and in
absolute and relative amounts. After it invocation, a bar plot built as a
ggplot object is returned
plotInOutFeatures(object, ...) ## S4 method for signature 'data.frame' plotInOutFeatures(object, absolute = FALSE) ## S4 method for signature 'TargetExperiment' plotInOutFeatures(object, absolute = FALSE, BPPARAM = bpparam())
object |
a data frame or a TargetExperiment. |
... |
additional parameters according to the function call |
absolute |
logical indicating if absolute frequency should be used. |
BPPARAM |
An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation. |
ggplot object.
see full example in TargetExperiment-class
Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar
## loading TargetExperiment object data(ampliPanel, package="TarSeqQC") ## Defining bam file, bed file and fasta file names and paths setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam", package="TarSeqQC", mustWork=TRUE) setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa", package="TarSeqQC", mustWork=TRUE) g<-plotInOutFeatures(ampliPanel)