View source: R/multi.bigwig.mean.R
multi.bigwig.mean | R Documentation |
This tools uses bigwigCompare
(see details) to perform the average between multiple bigWig files in a multi-step process.
multi.bigwig.mean(
sample.config,
output.dir = file.path(getwd(), "merged_bigWigs"),
bin.size = 50,
merged.suffix = paste0("_merged_bs", format(ceiling(bin.size), scientific = FALSE)),
out.file.format = "bigwig",
number.of.processors = 4,
bigwigCompare = "bigwigCompare",
return.log = FALSE,
verbose = TRUE
)
sample.config |
A data.frame or a string indicating the path to a table. The table/data.frame must contain in the first column the file list, while the second column the group to which belong each file. Files belonging to the same group will be merged together. The group name corresponds to the name of the corresponding output file. |
output.dir |
String of the path to the output directory. Default: |
bin.size |
Size of the bins in base-pairs (bp). Default: |
merged.suffix |
Suffix to use for the resulting output files: <group.id><suffix><extension>. Default: |
out.file.format |
Output file format. Possible choices: "bigWig", "bw", "bedGraph", "bdg". Default: |
number.of.processors |
Number of CPUs to use. Default: |
bigwigCompare |
String of the path to the |
return.log |
Logic value to define whether the log list of the |
verbose |
Logic value to define whether the function should print messages. Default: |
For details on bigwigCompare
visit: https://deeptools.readthedocs.io/en/develop/content/tools/bigwigCompare.html
A list of vectors with the commands used to run bigwigCompare
at each step. Each element is one group ID.
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