csaw.save.plots: Output of csaw analysis
In ArnaudDroitLab/ef.utils: Eric Utilities

Creates and saves plots and tables for csaw analysis:

Fragements lengths.pdf: A plot of fragments (reads) lengths in all bam files.
Window size.pdf: A cross-correlation plot of the efficiency of the ChIP-seq data.
Window size (zoom).pdf: A zommed version of "Window size.pdf".
Effect of filtering.pdf: A histogram of the counted reads, with lines representing background and filtering.
Normalization efforts.pdf: MA plots of the effect of normalization between the first file and every others.
TopTags results.txt: The best results of test.diff.binding.
Representative windows (differential binding).txt: Table of the most representative windows, by "differential binding" clustering method, after the correction for multiple testing.
LogFC of best windows in each cluster.txt: For each window cluster, the LogFC of the best windows, by "differential binding" clustering method, after the correction for multiple testing.
Representative windows (promoter-based).txt: Table of the most representative windows, by "promoter-based" clustering method, after the correction for multiple testing.
LogFC of best windows in each cluster (promoter-based).txt: For each window cluster, the LogFC of the best windows, by "promoter-based" clustering method, after the correction for multiple testing.
csaw_clusters.gz: The zipped table of results.

1
2
3

csaw.save.plots(list.reads.to.counts, list.reads.filter,
  list.normalization.factors, results, list.multiple.testing, annotations,
  output.dir)

`list.reads.to.counts`	List returned by `reads.to.counts`.
`list.reads.filter`	List returned by `filter.reads.to.counts`.
`list.normalization.factors`	List returned by `normalize.factors`.
`results`	Results of `test.diff.binding`.
`list.multiple.testing`	List returned by `multiple.testing`
`annotations`	The annotations to use.
`output.dir`	The name of the directory where to save the files and graphs.