diagplotFiltered: Diagnostic plot for filtered genes

In pmoulos/metaseqR2-local: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Diagnostic plot for filtered genes

Description

This function plots a grid of four graphs depicting: in the first row, the numbers of filtered genes per chromosome in the first column and per biotype in the second column. In the second row, the percentages of filtered genes per chromosome related to the whole genome in the first columns and per biotype in the second column.

Usage

    diagplotFiltered(x, y, output = "x11", path = NULL, ...)

Arguments

x	an annotation data frame like the ones produced by getAnnotation. x should be the filtered annotation according to metaseqR's filters.
y	an annotation data frame like the ones produced by getAnnotation. y should contain the total annotation without the application of any metaseqr filter.
output	one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf" or "ps".
path	the path to create output files.
...	further arguments to be passed to plot devices, such as parameter from par.

Value

The filenames of the plots produced in a named list with names the which.plot argument. If output="x11", no output filenames are produced.

Author(s)

Panagiotis Moulos

Examples

data("mm9GeneData",package="metaseqR2")
y <- mm9GeneCounts[,c(1:6,8,7)]
x <- y[-sample(1:nrow(y),1000),]
diagplotFiltered(x,y)

pmoulos/metaseqR2-local documentation built on May 21, 2024, 3:46 a.m.