Diagnostic plot for filtered genes

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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

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

Arguments

x

an annotation data frame like the ones produced by get.annotation. x should be the filtered annotation according to metaseqR's filters.

y

an annotation data frame like the ones produced by get.annotation. 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

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y <- get.annotation("mm9","gene")
x <- y[-sample(1:nrow(y),10000),]
diagplot.filtered(x,y)

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