repMeans {MKmisc} | R Documentation |
Compute mean of replicated spots
Description
Compute mean of replicated spots where additionally spot flags may incorporated.
Usage
repMeans(x, flags, use.flags = NULL, ndups, spacing, method, ...)
Arguments
x |
matrix or data.frame of expression values |
flags |
matrix or data.frame of spot flags; must have same dimension as |
use.flags |
should flags be included and in which way; cf. section details |
ndups |
integer, number of replicates on chip. The number of rows of
|
spacing |
the spacing between the rows of 'x' corresponding to
replicated spots, |
method |
function to aggregate the replicated spots. If missing, the mean is used. |
... |
optional arguments to |
Details
The incorporation of spot flags is controlled via argument use.flags
.
NULL
: flags are not used; minimum flag value of replicated
spots is returned
"max"
: only spots with flag value equal to the maximum flag value of
replicated spots are used
"median"
: only spots with flag values larger or equal to median of
replicated spots are used
"mean"
: only spots with flag values larger or equal to mean of replicated
spots are used
Value
LIST with components
exprs |
mean of expression values |
flags |
flags for mean expression values |
Note
A first version of this function appeared in package SLmisc.
Author(s)
Matthias Kohl Matthias.Kohl@stamats.de
See Also
Examples
## only a dummy example
M <- matrix(rnorm(1000), ncol = 10)
FL <- matrix(rpois(1000, lambda = 10), ncol = 10) # only for this example
res <- repMeans(x = M, flags = FL, use.flags = "max", ndups = 5, spacing = 20)