proteomics (version 0.2)

meetSelection: Data parsing -- from Proteom Discover v1.4

Description

Has been tested with PD v1.4

Usage

meetSelection(dwide, ch, ref)

Arguments

dwide

raw data from a PD export.

ch

the column names which hold the reporter ion intensities.

ref

the colmun name which holds the reporter ion intesities of the reference channel.

Details

This is a rather neat function that allows to get data from an export form the software Proteom Discoverer into R and parsed into a reasonable data frame such one can work with it. It will also add a few statistics and create unique identifiers for all identified peptides. You may argue that this functionality alone is worth the import of the whole package.

Examples

## Not run: 
# bio1 <- read.csv("my-proteome-discoverer-v1.4-export-experiment-1.csv")
# bio2 <- read.csv("my-proteome-discoverer-v1.4-export-experiment-2.csv")
# run1 <- droplevels(bio1[bio1$Quan.Usage == "Used",])
# run2 <- droplevels(bio2[bio2$Quan.Usage == "Used",])
# channels <- c("X113", "X114", "X115", "X116", "X117", "X118", "X119", "X121")
# reference <- c("X121")
# 
# run1 <- meetSelection(run1, channels, reference)
# run2 <- meetSelection(run2, channels, reference)
# 
# run1$experiment <- factor(1, levels=1:2, labels=c("iTRAQ-1", "iTRAQ-2"))
# run2$experiment <- factor(2, levels=1:2, labels=c("iTRAQ-1", "iTRAQ-2"))
# runs <- rbind(run1, run2)
# ## End(Not run)