Divides the genes that were not included in the top window in windows of the same size with decreasing mean expression levels.
A list, containing the top window generated by
An integer, indicating the number of bins to be used.
An integer, indicating the number of genes to be included
in each window. Ignored if
A boolean. Should the function print a message about window size or the number of windows created?
Two binning methods are available:
window_number: Divides the genes into the number of windows specified.
window_size: Divides the genes into windows of the size specified.
This function adds a bin number column to the data frame.
This function is designed to take the list output by the
extract_top_window function as an argument, operating only on the second element
of it. Once the genes in it have been binned, both elements of the list are bound
together in a data frame and returned. The output contains a new column
which indicates the window number assigned to each gene.
A data frame containing the binned genes.
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library(magrittr) expMat <- matrix( c(1, 1, 1, 1, 2, 3, 0, 1, 2, 0, 0, 2), ncol = 3, byrow = TRUE, dimnames = list(paste("gene", 1:4), paste("cell", 1:3)) ) calculate_cvs(expMat) %>% define_top_genes(window_size = 1) %>% bin_scdata(window_number = 2) calculate_cvs(expMat) %>% define_top_genes(window_size = 1) %>% bin_scdata(window_size = 1)
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