gcBoxplot: Plot GC dependency of probe intensities

In jotsetung/generalgcrma: GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.

Description

Creates boxplots depicting the dependency of probe intensities on a specific nucleotide content (e.g. G and C content) of the probes' sequences.

Usage

gcBoxplot( x, keep.pattern, exclude.pattern, ... )

plotNucleoCont(x, sequences, nt = c("C", "G"), log_trans= TRUE, center=FALSE, ylim=NULL, jahcol=FALSE)

Arguments

x	The AffyBatch object, a matrix or a numeric vector with probe intensities.
keep.pattern	pattern to restrict the boxplots to probes of specific probe sets. If not defined all pm probes will be used.
exclude.pattern	pattern to be used to exclude probes for specific probe sets. If not defined all pm probes will be used.
...	these args are passed to plotNucleoCount
sequences	The probe sequences with the same order and length as x if x is not an AffyBath.
nt	the nucleotide(s) for which the plot should be generated. Allowed values are A, C, G and T.
log_trans	log2 transform probe intensity values (Default is TRUE)
center	boxplot centered on overall intensity average (mean(x)) (Default is FALSE)
ylim	allows to manually specify the ylim, or to calculate ylim from the data (default).
jahcol	use fancy colramp to visualise probes nucleotide content (Default is FALSE).

Details

Creates boxplots with the average intensities for probes with the same G and C (or other nucleotides) content. If x is a matrix the probe sequences have to be submitted using the sequences parameter. Intensities in the rows of the matrix have to match with the sequences of the probes. The parameters keep.pattern and exclude.pattern can be used for e.g. custom CDF environments, like for the Exon microarrays, to generate the plot exclusively for background probes (e.g. by defining keep.pattern="bg" if the probe set names for background probes can be identified by an bg). The function assume data in natural scale as input and will default apply a log2 transform on it. Make sure to set the log_trans argument to FALSE if you whish to input already log2 transformed data.

Value

creates boxplots.

Author(s)

Johannes Rainer, Julien Lelong

References

Rainer J, Lelong J, Bindreither D, Mantinger C, Ploner C, Geley S, Kofler R. (2012) Research resource: transcriptional response to glucocorticoids in childhood acute lymphoblastic leukemia. Mol Endocrinol. 2012 Jan;26(1):178-93.

http://bioinfo.i-med.ac.at

jotsetung/generalgcrma documentation built on May 19, 2019, 9:41 p.m.