nucleotidePositionPlot: Nucleotide position dependent intensities

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

Description

Plots the average intensity of all probes with a specific nucleotide per position.

Usage

nucleotidePositionPlot( x, keep.pattern, exclude.pattern ,... )
plotNucleoPos(x, sequences, log_trans = TRUE, center=FALSE)

Arguments

x	The AffyBatch object, a matrix or a numeric vector with probe intensities.
keep.pattern	pattern to restrict the plot 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.
sequences	The probe sequences with the same order and length as x if x is not an AffyBath.
log_trans	log2 transform probe intensity values (Default is TRUE)
center	mean probe intensity centered on overall intensity average (mean(x))(Default is FALSE).
...	Additional arguments passed to the plotNucleoPos function.

Details

Creates a plot of the averaged intensities of probes with a specific nucleotide at each position along the probe sequence.

Value

Creates a plot

Author(s)

Julien Lelong, Johannes Rainer

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.