as.normalizedMatrix {EnrichedHeatmap} | R Documentation |
Convert a normal matrix to a normalizedMatrix object
as.normalizedMatrix(mat, k_upstream = 0, k_downstream = 0, k_target = 0, extend, signal_name = "signals", target_name = "targets", background = NA, smooth = FALSE, smooth_fun = default_smooth_fun, keep = c(0, 1), trim = NULL)
mat |
a matrix generated by other software. |
k_upstream |
number of windows in the upstream. |
k_downstream |
number of windows in the downstream. |
k_target |
number of windows in the target. |
extend |
extension to the target. The length should be 1 (if one of |
signal_name |
the name of signal regions. It is only used for printing the object. |
target_name |
the name of the target names. It is only used for printing the object. |
background |
the background value in the matrix. |
smooth |
whether apply smoothing on rows in the matrix. |
smooth_fun |
the smoothing function that is applied to each row in the matrix. This self-defined function accepts a numeric vector (may contain |
keep |
percentiles in the normalized matrix to keep. The value is a vector of two percent values. Values less than the first percentile is replaces with the first pencentile and values larger than the second percentile is replaced with the second percentile. |
trim |
deprecated, please use |
If users use the matrix from other software, they can use this function to convert it to the normalizedMatrix
object
and visualize it afterwards.
A normalizedMatrix
object.
z.gu@dkfz.de
# There is no example NULL