Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples
plot boxplots of the mean values of ChIPseq experiments on the annotations given to the extractBinding method
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34  boxplotSpike(theObject, col = NULL, rawFile = FALSE,
rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE,
notch = TRUE, mean_with_sd = FALSE, mean = FALSE,
median = FALSE, boxplot = FALSE, jitter = FALSE, plot = TRUE,
verbose = FALSE)
## S4 method for signature 'ChIPSeqSpikeDataset'
boxplotSpike(theObject, col = NULL, rawFile =
FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, ylab
= NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE, mean_with_sd = FALSE,
mean = FALSE, median = FALSE, boxplot = FALSE, jitter = FALSE, plot = TRUE,
verbose = FALSE)
## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
boxplotSpike(theObject, col = NULL,
rawFile = FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE,
mean_with_sd = FALSE, mean = FALSE, median = FALSE, boxplot = FALSE,
jitter = FALSE, plot = TRUE, verbose = FALSE)
## S4 method for signature 'ChIPSeqSpikeDatasetList'
boxplotSpike(theObject, col = NULL, rawFile
= FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE,
ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE, mean_with_sd =
FALSE, mean = FALSE, median = FALSE, boxplot = FALSE, jitter = FALSE,
plot = TRUE, verbose = FALSE)
## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
boxplotSpike(theObject, col = NULL,
rawFile = FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE,
mean_with_sd = FALSE, mean = FALSE, median = FALSE, boxplot = FALSE,
jitter = FALSE, plot = TRUE, verbose = FALSE)

theObject 

col 
Vector of colors for each experiment. Default is NULL. 
rawFile 
If TRUE, use the untransformed data. Not available in boost mode. Default is FALSE. (see details) 
rpmFile 
If TRUE, use the RPM scaled data. Not available in boost mode. Default is FALSE. (see details) 
bgsubFile 
If TRUE, use the input subtracted data. Not available in boost mode. Default is FALSE. (see details) 
revFile 
If TRUE, use the RPM reverted data. Not available in boost mode. Default is FALSE. (see details) 
spiked 
If TRUE, use the spiked data. Default is TRUE. (see details) 
ylab 
Character string of the name of the yaxis. Default is NULL. 
outline 
Logical indicating if outliers are shown. Default is TRUE. 
violinPlot 
Logical indicating if a violin plot representation is used. Default is FALSE. 
notch 
Logical indicating if confidence intervals are shown. Default is TRUE. 
mean_with_sd 
Logical indicating if the mean and standard deviation are shown on the violin plot. Default is FALSE. 
mean 
Logical indicating if the mean is shown on the violin plot. Default is FALSE. 
median 
Logical indicating if the median is shown on the violin plot. Default is FALSE. 
boxplot 
Logical indicating if boxplot is shown on the violin plot. Default is FALSE 
jitter 
Logical indicating if each mean values is represented as a point on the violin plot. Default is FALSE. 
plot 
Logical indicating if the boxplot should be plotted. Default is TRUE. 
verbose 
Logical indicating if processing messages are shown. Default is FALSE. 
The 'rawFile', 'rpmFile', 'bgsubFile', 'revFile', 'spiked' parameters indicate if the untransformed, RPM scaled, input DNA subtracted, RPM reversed or spiked data should be plotted. This option is only available if not in boost mode (see ?spikePipe for details on what these steps are).
Return a list with the components 'stats', 'n', 'conf', 'out', 'group' and 'names'. See ?boxplot for details.
ChIPSeqSpikeDataset
: Method for signature theObject=
'ChIPSeqSpikeDataset'
ChIPSeqSpikeDatasetBoost
: Method for signature theObject=
'ChIPSeqSpikeDatasetBoost'
ChIPSeqSpikeDatasetList
: Method for signature theObject=
'ChIPSeqSpikeDatasetList'
ChIPSeqSpikeDatasetListBoost
: Method for signature theObject=
'ChIPSeqSpikeDatasetListBoost'
Nicolas Descostes
spikeDataset
spikePipe
plotProfile
plotTransform
plotHeatmaps
plotCor
1 2 3 4 5 6 7  data("result_extractBinding")
boxplotSpike(csds)
boxplotSpike(csds, outline = FALSE, violinPlot = TRUE)
boxplotSpike(csds, outline = FALSE, violinPlot = TRUE, mean = TRUE, jitter =
TRUE)
boxplotSpike(csds, rawFile = TRUE, rpmFile = TRUE, bgsubFile = TRUE, revFile =
TRUE, spiked = TRUE, outline = FALSE, violinPlot = TRUE)

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