repMeans {SLmisc} | R Documentation |
Compute mean of replicated spots where additionally spot flags may incorporated.
repMeans(x, flags, use.flags = NULL, ndups, spacing)
x |
matrix or data.frame of expression values |
flags |
matrix or data.frame of spot flags; must have same dimension as x |
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
x must be divisible by ndups |
spacing |
the spacing between the rows of 'x' corresponding to
replicated spots, spacing = 1 for consecutive spots;
cf. function unwrapdups in package
"limma" |
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
LIST with components
exprs |
mean of expression values |
flags |
flags for mean expression values |
Dr. Matthias Kohl (SIRS-Lab GmbH) kohl@sirs-lab.com
## 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)