This function represent a high-level entry-point for performing a Scaffold analysis
1 2 3 4 5 6 7 8 9 10 | run_scaffold_analysis(
files.list,
ref.file,
landmarks.data,
col.names,
out.dir = "scaffold_result",
process.clusters.data = TRUE,
downsample.to = 1000,
...
)
|
files.list |
Character vector. The list of files to process |
ref.file |
The name of the file to be used as reference (i.e. the first file to be processed, which will determine the position of the landmarks in all subsequent maps) |
landmarks.data |
The landmarks data as returned by |
col.names |
A character vector of column (i.e. marker) names to be used for the analysis. These columns have to be present in all the files |
out.dir |
The name of the output directory |
process.clusters.data |
If this is |
downsample.to |
The number of events to target for downsampling when processing the clusters data. This is only used if
|
... |
Additional parameters passed to |
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