Like in paper https://www.pnas.org/content/111/16/5980 (Fig. 4).
inc_overlap( .data, .fun, .step = 1000, .n.steps = 10, .downsample = FALSE, .bootstrap = NA, .verbose.inc = TRUE, ... )
The data to be processed. Can be data.frame, data.table, or a list of these objects.
Every object must have columns in the immunarch compatible format. immunarch_data_format
Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects.
Note: each connection must represent a separate repertoire.
Function to compute overlaps. e.g.,
Either an integer or a numeric vector.
In the first case, the integer defines the step of incremental overlap.
In the second case, the vector encodes all repertoire sampling depths.
Integer. Number of steps if
If TRUE then perform downsampling to N clonotypes at each step instead of choosing the top N clonotypes.
Pass NA to turn off any bootstrapping, pass a number to perform bootstrapping with this number of tries.
Logical. If TRUE then show output from the computation process.
Other arguments passed to
List with overlap matrices.
data(immdata) ov <- repOverlap(immdata$data, "inc+overlap", .step = 100, .verbose.inc = FALSE, .verbose = FALSE) vis(ov)