TileCalcWinScr2 {TileShuffle} | R Documentation |
Wrapper function for calculating window scores using different functions.
TileCalcWinScr2(int, win.st, win.len, score.function=c("mean", "trimmed", "median"))
int |
A numeric vector containing one or more probe
scores (i.e. intensities or log-fold changes). |
win.st |
An integer vector containing one or more window
start positions in int . |
win.len |
An integer vector containing one or more window
lengths. It must be of same length as win.st . |
score.function |
Function to calculate windows scores over the
log2 -intensities or log2 -fold changes of the
corresponding probes, i.e., arithmetic average
(score.function = "mean"), arithmetic mean trimmed by the
minimal and maximal value (score.function = "trimmed"),
or the median (score.function = "median"). Note that the
definition of trimmed mean differs from the common one with given
percentile ranges. Moreover, the resulting scores with trimmed
mean may only differ from the mean only in case of windows that
contain more than two probes. The latter two scoring functions
are recommended due to their higher robustness against outliers.
However, due to the higher calculation costs, the running time
increases by selecting "trimmed" or "median". Note that the function
is given as character . |
Wrapper function for calculating window scores using different functions on
probe scores with given start positions and window lengths. In case of few
but longer windows, this function is superior to TileCalcWinScr
which is optimized for short windows.
A numeric
vector
containing the calculated window
scores for the given start positions. Note that windows of length
zero are reported with a window score of NA
. Moreover, probe
scores with the value NA
are excluded from the calculation.