More changes.
Allow sliding mean to apply over separate spaces in RangedData slot
Major overhaul, need to test now.
Add warning message about smoothing over multiple spaces, fix typo bug.
Expanded explanations of arguments and function requirements.
Add a details section to explain argument requirements.
Change log-check "stop" to a warning, fix a change in first stop
Improve Zpep track for normalization. 
Adds a function to compute Z-scales from peptide sequences if Z-scale
values are not found in the featureRange slot of the peptideSet
argument.

Removes some redundant or unnecessary pieces of code and comments. 

Adds a check to the method argument.
Fix bug in how normalization data is added to "preproc" info.
Cleaned up the package and fixed a few bugs.
Merge branch 'devel' into devel-new

Conflicts:
	NAMESPACE
	R/NormalizeArray.R
	R/slidingMean.R
	R/summarizePeptides.R
Fix header manipulation in .sanitize.mapping.file
Fix function name error.
edit name of argument checking function
edit namespace to import "rbind" method from IRanges, required for
sliding mean function.
add "tolower" to grep of visit factor
Change "cat" to "message" (Bioconductor standard)
simplify function to compute left-tail subject-specific FDR estimates.
Merge branch 'devel-new'

Conflicts:
	R/slidingMean.R
	man/summarizePeptides.Rd
	src/symbols.rds