cbs.segment_all | R Documentation |
Generate the segmented profile for each cell in the input directory with CBS. (Including GC correction)
cbs.segment_all(input_file_dir, Nk = "5k", gc, alpha, nperm, undo.SD, min.width, method = "multiplier", genome = "hg")
input_file_dir |
The directory that contains the bin count files for all cells. For example, one bin count file for a cell is CJA1023.varbin.20k.txt |
Nk |
Default value: 5k. It denotes the number of bins. 5000 = 5k, 10000 = 10k, ... |
gc |
The GC content table. |
alpha |
Parameter alpha defined in DNAcopy package. |
nperm |
Parameter nperm defined in DNAcopy package. |
undo.SD |
Parameter undo.SD defined in DNAcopy package. |
min.width |
Parameter min.width defined in DNAcopy package. |
method |
Default: "multiplier" to transform the ratio data to integer CN state. When genome is hg-dm hybrid, set method as "dmploidies" to use dm plodies as reference. |
genome |
Default: "hg" (Human genome). hg-dm hybrid genome: "hgdm". |
The list containing seg.quantal and ratio.quantal matrix for all cells in the input_file_dir.
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