countNoOfCommonPeptides {wrProteo}

Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides. The in-silico digestion may be performed separately using the package cleaver. Note: input must be list (or multiple names lists) of proteins with their respective peptides (eg by in-silico digestion).

Description

Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides

Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides. The in-silico digestion may be performed separately using the package cleaver. Note: input must be list (or multiple names lists) of proteins with their respective peptides (eg by in-silico digestion).

Usage

countNoOfCommonPeptides(
  ...,
  prefix = c("Hs", "Sc", "Ec"),
  sep = "_",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

...

(list) multiple lists of (ini-silico) digested proteins (typically protein ID as names) with their respectice peptides (AA sequence), one entry for each species

prefix

(character) optional (species-) prefix for entries in '...', will be only considered if '...' has no names

sep

(character) concatenation symbol

silent

(logical) suppress messages

debug

(logical) display additional messages for debugging

callFrom

(character) allow easier tracking of message(s) produced

Value

This function returns a list with $byPep as list of logical matrixes for each peptide (as line) and unique/shared/etc for each species; $byProt as list of matrixes with count data per proten (as line) for each species; $tab with simple summary-type count data

See Also

readFasta2 and/or cleave-methods in package cleaver

Examples

## The example mimics a proteomics experiment where extracts form E coli and 
## Saccharomyces cerevisiae were mixed, thus not all peptdes may occur unique.  
(mi2 = countNoOfCommonPeptides(Ec=list(E1=letters[1:4],E2=letters[c(3:7)],
  E3=letters[c(4,8,13)],E4=letters[9]),Sc=list(S1=letters[c(2:3,6)], 
  S2=letters[10:13],S3=letters[c(5,6,11)],S4=letters[c(11)],S5="n")))
##  a .. uni E, b .. inteR, c .. inteR(+intra E), d .. intra E  (no4), e .. inteR, 
##  f .. inteR +intra E   (no6), g .. uni E, h .. uni E  no 8), i .. uni E, 
##  j .. uni S (no10), k .. intra S  (no11), l .. uni S (no12), m .. inteR  (no13)
lapply(mi2$byProt,head)
mi2$tab