- element.x
which element of AssayData
to use (for signal channel 1) for a given ExpressionSet
input (default is "exprs")
- element.y
which element of AssayData
to use (for signal channel 2) for a given ExpressionSet
input (default is "exprs2")
- sample
which element of sampleNames
to use as data (default is 1). Can be a character matching a sample name or simply an integer indicating which sample to choose.
- feature
which element of featureData
to use as plotting feature (default is 1). Can be a character matching varLabel
or simply an integer indicating which feature to choose.
- feature.random
which element of featureData
to use to identify random probes (default is "TYPE"). Can be a character matching varLabel
or simply an integer indicating which feature to choose.
- which.random
an integer vector specifying which rows of data correspond to random probes. if NULL (default), the function will attempt to identify random probes using featureData
.
- random.flag
a character specifying the label for random probes in feature.random
from featureData
. Default is "RAND".
- na.rm
logical; if TRUE (default), missing values are removed from x
. If FALSE any missing values cause an error.
- limit
numerical input specifying the maximum number of points to plot (default is 10,000). if NULL, all points will be used.
- cutoff
a numerical input specifying the value below which signal intensities from channel 1 can be considered "failed" probes. If NULL (default), the function will attempt to calculate a cutoff from random probe information.
- cutoff2
a numerical input specifying the value below which signal intensities from channel 2 can be considered "failed" probes. If NULL (default), the function will attempt to calculate a cutoff from random probe information.
- main
an overall title for the plot: see title
.
- xlab
a title for the x axis (default is "Fragment size (bp)"): see title
.
- ylab
a title for the y axis for signal channel 1 (default is "log(MspI)"): see title
.
- ylab2
a title for the y axis for signal channel 2 (default is "log(HpaII)"): see title
.
- cex
numerical value (default is 0.2) giving the amount by which plotting text and symbols should be scaled relative to the default.
- \dots
other arguments to be passed to plot
. See plot
.