- Create dependencies installation script
- Update R version on TPP server

- TSV export
	- norm median intensities
	- specify whether intensities are raw/norm 		

- peptide length distribution plot
	
- multiple issues (GRAPHICS) if only one identified protein.

- use "plyr" and ddply

- speed up parsing. update/get rid off .getProgenesisCsvExpressionColIndices()

- normalization methods
	- quantile normalization
	- rt bin normalization (applying coarser binning) 

- heatmap
	# don't display discarded conditions in legend

- map scaffold PTM results to progenesis data

- scaffold ptm full support
	- parse scaffold ptm annotations 
		- convert scaffold ptm annotations to ptm coordinates
		- motifX support 		

- ptm export 
	- add residue to ptm coordinate export

### SOLVED

### - write column description for peptide and protein tsv. 

### - compatibility with fractionated data

### - write manual
### 	- protein level LFQ
### 	- Phospho (PTM) LFQ
### 	- TMT

### - automatic mass accuracy filter
### - default output dir to input dir
### - hCLust feature limit when --EP option
### - peptide length filter
### rt normalization failure
###./safeQuant.R -i /Volumes/pcf01\$/Schmidt_Group/tmp/peptides_FILTERED.csv	


### - PDF export
### 	- Protein level Hierarchical CLustering
### 		 - Ratio Profile hierarchical clustering 

### - protein inference 
### 	- cannot use "peptide measurement exports" as feature are mapped to peptides. The same feature is listed multiple times
 
### - graphic showing number of peptides per r.t. (ideally uniform distribution)
###	- alt. show cumulative as a function of r.t 
### - Troubleshoot getAllCV and getCV

### - update getMotifX 
###	 getMotifX <- function(modifAnnot,peptide,proteinSeq, motifLength=4){ ->  getMotifX <- function(modifPos,peptide,proteinSeq, motifLength=4){ 

### - expDesign, keep condition names unless conditions are mixed 

### - add "examples" to -h option