| makePlot.gene.assignment.rates {QoRTs} | R Documentation |
Plots the rate at which reads are assigned into various categories.
makePlot.gene.assignment.rates(plotter, debugMode, singleEndMode, ...)
plotter |
A |
debugMode |
Logical. If TRUE, debugging data will be printed to the console. |
singleEndMode |
Logical. Determines whether the dataset consists of single-ended reads. By default this is determined from the data. Thus, this parameter should never need to be set by the user. |
... |
Arguments to be passed to methods, such as
graphical parameters (see |
For each bam-file, this function plots the rate (y-axis) for which the bam-file's read-pairs are assigned to the given categories.
The categories are:
Unique Gene: The read-pair overlaps with the exonic segments of one and only one gene. For many downstream analyses tools, such as DESeq, DESeq2, and EdgeR, only read-pairs in this category are used.
Ambig Gene: The read-pair overlaps with the exons of more than one gene.
No Gene: The read-pair does not overlap with the exons of any annotated gene.
No Gene, Intronic: The read-pair does not overlap with the exons of any annotated gene, but appears in a region that is bridged by an annotated splice junction.
No Gene, 1kb from gene: The read-pair does not overlap with the exons of any annotated gene, but is within 1 kilobase from the nearest annotated gene.
No Gene, 10kb from gene: The read-pair does not overlap with the exons of any annotated gene, but is within 10 kilobases from the nearest annotated gene.
No Gene, middle of nowhere: The read-pair does not overlap with the exons of any annotated gene, and is more than 10 kilobases from the nearest annotated gene.
data(res,package="QoRTsExampleData");
plotter <- build.plotter.colorByGroup(res);
makePlot.gene.assignment.rates(plotter)
## Starting: Gene Assignment Rates plot.
## Finished: Gene Assignment Rates plot.[time: 2016-01-28 16:32:57],[elapsed: 0.04 secs]