sgibb

bin <- function(x)x

setGeneric("bin", function(x) standardGeneric("bin"))
setMethod("bin", "matrix", function(x)x)

i <- 1:10
m <- matrix(1:10, nrow=2)

showMethods("bin")
# Function: bin (package .GlobalEnv)

sgibb

setClass("ondiskvec",
    slots=list(path="character", n="numeric"),
    prototype=list(path=character(), n=numeric())
)

ondiskvec <- function(x, path=tempfile()) {
    writeBin(as.double(x), path, size=8L)
    new("ondiskvec", path=path, n=length(x))
}

sgibb

library("mzR")
library("msdata")
library("rhdf5")
library("digest")
.sha1 <- function(x)vapply(x, digest::sha1, NA_character_, USE.NAMES=FALSE)

setClass(
    "Backend",
    contains="VIRTUAL"
)

sgibb

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

sgibb

sgibb

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

#!/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

sgibb

##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 

sgibb

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)),

sgibb

# 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`)