sgibb

library("synapter")
library("synapterdata")

###########################################################################
## some boring stuff to prepare the Synapter object
###########################################################################

fasfile <- synapterdata::getFasta()
mstrfile <- synapterdata::getMaster()
pepfile <- synapterdata::getMSeFinalPeptide()[2]

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importSIMS <- function(path) {
  stopifnot(file.exists(path) && file.info(path)$isdir)

  ## find all txt files 
  files <- list.files(path, pattern="^.*\\.txt$", full.names=TRUE, recursive=TRUE)
  files <- normalizePath(files)

  ## read metadata (first 8 lines) of the SIMS file
  ll <- lapply(files, function(f)readLines(f, n=8))

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# Cross Matching Example

```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(fig.height=10, fig.width=14, fig.path="figure/crossmatching/", cache=TRUE, autodep=TRUE, tidy=FALSE)
```
## Default Synapter Preprocessing

(same as in `synergise`)

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# Ion Mobility Example

```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(fig.height=10, fig.width=14, fig.path="figure/ionmobility/", cache=TRUE, autodep=TRUE, tidy=FALSE)
```
## Default Synapter Preprocessing

(same as in `synergise`)

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library("synapter")
library("MSnbase")
load_all()

combMSnSet <- readRDS("refCombMSNSet.RDS")

plotProteomes <- function(x,
                          xlim=log2(range(exprs(x), na.rm=TRUE)),
                          ylim=c(-4, 4),
                          xlab=expression(log[2](B)),

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##TITLE=  XMASS Parameter file
##JCAMPDX=  5.0
##DATATYPE=  CONTINUOUS MASS SPECTRUM
##ORIGIN=  XMASS, Bruker-Daltonics (USA) and Bruker-Daltonik (GER)
##OWNER=  TOF User
##SPECTROMETER/DATASYSTEM=  Bruker Flex Series
##.SPECTROMETER TYPE=  TOF
##.INLET=  DIRECT
##.IONIZATION MODE=  LD+
##$ACQMID= 0 

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#!/bin/sh
PROCESSPID=${1}
pidstat -urIh -p ${PROCESSPID} 1 1 | grep -v "^Linux\|^ *$" > memstat.txt && pidstat -urIh -p ${PROCESSPID} 60 | grep -v "^#\|^ *$\|^Linux" | tee -a memstat.txt

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Keybase proof

I hereby claim:

• I am sgibb on github.
• I am sgibb (https://keybase.io/sgibb) on keybase.
• I have a public key whose fingerprint is 22C0 E8AC A81A 3A13 C788 BCC4 ECAA 2C0A 2843 245B

To claim this, I am signing this object:

sgibb

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library("MALDIquant")

setClass("MassSpectrumOnDisk",
         slots=list(path="character", n="numeric"),
         prototype=list(mass=numeric(), intensity=numeric(), metaData=list(),
                        path=character(), n=numeric()),
         contains="AbstractMassObject")

## overwrite default validation method (checks for non-empty intensity etc)
## needs to be rewritten obviously