Description Usage Arguments Details Value Author(s) Examples
Functions to detect possible RNA degradation.
1 2 3 4 5 6 7 | AffyRNAdeg(xps.data, treename = "*", qualopt = "raw", log.it = TRUE)
summaryAffyRNAdeg(rna.deg, signif.digits=3)
plotAffyRNAdeg(rna.deg, transform = "shift.scale", col = NULL, summary = FALSE, add.legend = FALSE, ...)
xpsRNAdeg(object, ...)
|
xps.data |
object of class |
treename |
vector of tree names to export. |
qualopt |
option determining the data to which to apply qualification, one of ‘raw’, ‘adjusted’, ‘normalized’. |
log.it |
logical, if TRUE, then probe data is log2 transformed. |
rna.deg |
|
signif.digits |
number of significant digits to show. |
transform |
transform data before plotting, one of "shift.scale", "shift.only", "none". |
col |
vector of colors for plot, length is number of samples. |
summary |
logical, if TRUE then the slope of |
add.legend |
logical or integer, if TRUE or larger than zero then a legend with the tree names will be drawn. |
object |
object of class |
... |
optional arguments to be passed to |
Since probes within a probeset are ordered directionally from the 5' end to the 3' end, it is possible to estimate the quality (degradation status) of the RNA.
Function AffyRNAdeg
averages the probe intensities by location in the
probeset, with the average taken over all probesets with identical number of
probes.
Function summaryAffyRNAdeg
produces a single summary statistic for
each array.
Function plotAffyRNAdeg
produces a side-by-side plot of the averaged
intensities. Option transform = "none"
shows the averaged intensities
for each array while option "shift" staggers the plots for individual arrays
vertically to make the display easier to read, and option "scale" normalizes
the averaged intensities so that the standard deviation is equal to one.
Setting parameter add.legend = TRUE
will add a legend containing all
tree names to the plot, while setting e.g. add.legend = 6
will only
show the first 6 tree names.
AffyRNAdeg
returns a list
with following components:
N |
number of probesets with identical number of probes |
sample.names |
names of samples, derived from affy batch object |
mns |
average intensity by probe position |
ses |
standard errors for probe position averages |
slope |
from linear regression of means.by.number |
pvalue |
from linear regression of means.by.number |
Christian Stratowa, adapted from package affy
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## Not run:
rnadeg <- xpsRNAdeg(rlm.all, treename="*", qualopt="raw")
plotAffyRNAdeg(rnadeg)
rnadeg <- AffyRNAdeg(rlm.all)
result <- summaryAffyRNAdeg(rnadeg)
## plot RNA degradation
plotAffyRNAdeg(rnadeg)
## plot slope of RNA degradation
plotAffyRNAdeg(rnadeg, summary = TRUE)
## End(Not run)
|
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