Description Usage Arguments Details Value Author(s) See Also Examples
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.
1 2 | 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
.
1 2 3 | dat <- dummyData()
smoothed <- runmedByCluster(y=dat$mat[,1], cluster=dat$cluster,
k=5, endrule="constant")
|
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