runmedByCluster | R Documentation |
Running median smoothing is applied independently to each cluster of genomic locations. Locations within the same cluster are close together to warrant smoothing across neighbouring locations.
runmedByCluster(y, x = NULL, cluster, weights = NULL, k = 5,
endrule = "constant", verbose = TRUE)
y |
A vector or matrix of values to be smoothed. If a matrix, each column represents a sample. |
x |
The genomic location of the values in y. |
cluster |
A vector indicating clusters of locations. A cluster is typically defined as a region that is small enough that it makes sense to smooth across neighbouring locations. Smoothing will only be applied within a cluster, not across locations from different clusters. |
weights |
weights used by the smoother. |
k |
integer width of median window; must be odd. See |
endrule |
character string indicating how the values at the
beginning and the end (of the data) should be treated. See
|
verbose |
Boolean. Should progress be reported? |
This function is typically called by smoother
, which is in
turn called by bumphunter
.
fitted |
The smoothed data values |
smoothed |
A boolean vector indicating whether a given position was smoothed |
spans |
The span used by the loess smoother. One per cluster. |
clusterL |
The number of locations in each cluster. |
smoother |
always set to ‘runmed’. |
Rafael A. Irizarry
smoother
, loessByCluster
. Also see runmed
.
dat <- dummyData()
smoothed <- runmedByCluster(y=dat$mat[,1], cluster=dat$cluster,
k=5, endrule="constant")
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