ruv_rle: RUV RLE Plot

In ruv: Detect and Remove Unwanted Variation using Negative Controls

Description

An RLE (Relative Log Expression) Plot

Usage

ruv_rle(Y, rowinfo = NULL, probs = c(0.05, 0.25, 0.5, 0.75, 0.95), ylim = c(-0.5, 0.5))

Arguments

Y	The data matrix. Rows are observations and columns are features (e.g. genes).
rowinfo	A dataframe of information about the observations. Should have the same number of rows as Y. This information will be included in the ggplot, and can be used for setting aesthetics such as color.
probs	The percentiles used to construct the boxplots. By default, whiskers are drawn to the 5th and 95th percentiles. Note that this is non-standard for boxplots.
ylim	Limits of the y axis. Defaults to (-0.5, 0.5) so that the plots are always on the same scale and can be easily compared.

Value

A ggplot.

Author(s)

Johann Gagnon-Bartsch

References

Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B., and Speed, T. P. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic acids research, 31(4):e15.

ruv documentation built on Aug. 31, 2019, 1:04 a.m.